EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Co-authors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.
EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics
EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.
concept_properties "EDAM concept properties"
EDAM_operation http://edamontology.org/operation_ "EDAM operations"
EDAM_topic http://edamontology.org/topic_ "EDAM topics"
EDAM_data http://edamontology.org/data_ "EDAM types of data"
EDAM_format http://edamontology.org/format_ "EDAM data formats"
EDAM http://edamontology.org/ "EDAM relations and concept properties"
Version in which a concept was made obsolete.
'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.
'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too.
'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format.
'A has_format B' defines for the subject A, that it has the object B as its data format.
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'.
'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject.
'A has_function B' defines for the subject A, that it has the object B as its function.
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts.
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject.
'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject.
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'.
'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument.
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined.
'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant).
'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject.
'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument.
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined.
'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant).
'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it.
'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource.
'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object.
Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined.
'A is_format_of B' defines for the subject A, that it is a data format of the object B.
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object.
'A is_function_of B' defines for the subject A, that it is a function of the object B.
Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used.
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object.
Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions.
'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B.
Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined.
'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B.
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'.
'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011).
'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments.
'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B.
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.
'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011).
'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it.
Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'.
'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).
A type of computational resource used in bioinformatics.
Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.
IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something.
EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information).
EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set).
IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity.
Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019).
Data does however not necessarily contain statements and not necessarily about an entity.
GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual.
A bioinformatics package or tool, e.g. a standalone application or web service.
A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.
An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.
A directory on disk from which files are read.
Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases.
Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee.
Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System).
A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).
Almost exact but limited to identifying resources.
An entry (retrievable via URL) from a biological database.
A specification of a chemical structure.
QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.
A QSAR quantitative descriptor (name-value pair) of chemical structure.
Non-sequence characters may be used for example for gaps and translation stop.
A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.
A molecular sequence and associated metadata.
This concept may be used for arbitrary sequence sets and associated data arising from processing.
A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
A character used to replace (mask) other characters in a molecular sequence.
Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
A label (text token) describing the type of sequence masking to perform.
The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.
The strand of a DNA sequence (forward or reverse).
This is used for such things as a report including the sequence identifier, type and length.
Basic or general information concerning molecular sequences.
How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived.
This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).
A report of sequence hits and associated data from searching a sequence database (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.
The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.
A report of hits from a search of a protein secondary or domain database.
Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.). In this way the query is classified as a member of a known protein family or group. See concepts under 'Protein features'.
Data files used by motif or profile methods.
A classifier of sequences such as a sequence motif, profile or other diagnostic element.
Alignment of exact matches between subsequences (words) within two or more molecular sequences.
A dotplot of sequence similarities identified from word-matching or character comparison.
Alignment of multiple molecular sequences.
Some simple value controlling a sequence alignment (or similar 'match') operation.
A value representing molecular sequence similarity.
Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score.
An informative report of molecular sequence alignment-derived data or metadata.
This is a broad data type and is used a placeholder for other, more specific types.
A profile-profile alignment (each profile typically representing a sequence alignment).
Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores.
Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment).
Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.
A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation.
Basic character data from which a phylogenetic tree may be generated.
As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments
The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.
A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.
Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.
The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).
The location and size of the secondary structure elements and intervening loop regions is usually indicated.
Predicted or actual protein topology represented as a string of protein secondary structure elements.
The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks).
Secondary structure assignment (predicted or real) of a protein.
Protein structure report (super-secondary)
Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
A report of predicted or actual super-secondary structure of protein sequence(s).
Alignment of the (1D representations of) secondary structure of two or more proteins.
Secondary structure alignment metadata (protein)
An informative report on protein secondary structure alignment-derived data or metadata.
This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.
An informative report of secondary structure (predicted or real) of an RNA molecule.
Alignment of the (1D representations of) secondary structure of two or more RNA molecules.
Secondary structure alignment metadata (RNA)
An informative report of RNA secondary structure alignment-derived data or metadata.
3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.
The coordinate data may be predicted or real.
An entry from a molecular tertiary (3D) structure database.
Results (hits) from searching a database of tertiary structure.
A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.
Alignment (superimposition) of molecular tertiary (3D) structures.
An informative report of molecular tertiary structure alignment-derived data.
A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison.
Some type of structural (3D) profile or template (representing a structure or structure alignment).
A 3D profile-3D profile alignment (each profile representing structures or a structure alignment).
An alignment of a sequence to a 3D profile (representing structures or a structure alignment).
Protein sequence-structure scoring matrix
Matrix of values used for scoring sequence-structure compatibility.
An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)).
An informative report about a specific amino acid.
An informative report about a specific peptide.
An informative report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.
The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types.
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.
An informative report on the 3D structural motifs in a protein.
This might include conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, role and functions etc.
Data concerning the classification of the sequences and/or structures of protein structural domain(s).
The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc.
Summary of structural domains or 3D folds in a protein or polypeptide chain.
An informative report on architecture (spatial arrangement of secondary structure) of a protein structure.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc.
Data on the effect of (typically point) mutation on protein folding, stability, structure and function.
Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with itself or some other molecule(s), which might be another protein, nucleic acid or some other ligand.
An informative report on a specific protein family or other group of classified proteins.
The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.
Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction.
An informative report about a specific nucleotide base.
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.
Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences.
This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).
An informative report on a particular locus, gene, gene system or groups of genes.
A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products.
A report on stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.
This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
An informative report on a specific chromosome.
An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes.
Report on matches to PCR primers and hybridization oligos in a nucleic acid sequence.
Data on a PCR assay or electronic / virtual PCR.
This is the raw data produced by a DNA sequencing machine.
Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.
Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.
An assembly of fragments of a (typically genomic) DNA sequence.
Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'.
Radiation hybrid scores (RH) scores for one or more markers.
Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.
An informative report on the linkage of alleles.
Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.
This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.
Information on a microarray experiment such as conditions, protocol, sample:data relationships etc.
Data on oligonucleotide probes (typically for use with DNA microarrays).
Serial analysis of gene expression (SAGE) experimental data
Output from a serial analysis of gene expression (SAGE) experiment.
Massively parallel signature sequencing (MPSS) experimental data
Massively parallel signature sequencing (MPSS) data.
Sequencing by synthesis (SBS) experimental data
Sequence tag profile (with gene assignment)
Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers.
Protein nuclear magnetic resonance (NMR) raw data.
Protein circular dichroism (CD) spectroscopic data
Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data.
Volume map data from electron microscopy.
This might include the location in the model of the known features of a particular macromolecule.
Annotation on a structural 3D model (volume map) from electron microscopy.
Two-dimensional gel electrophoresis image.
A set of peptide masses (peptide mass fingerprint) from mass spectrometry.
Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database.
An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway.
A map (typically a diagram) of a biological pathway.
A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper.
Basic information, annotation or documentation concerning a workflow (but not the workflow itself).
A biological model which can be represented in mathematical terms.
A value representing estimated statistical significance of some observed data; typically sequence database hits.
Resource definition for an EMBOSS database.
Information on a version of software or data, for example name, version number and release date.
Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.
A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.
An index of data of biological relevance.
A report of an analysis of an index of biological data.
Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.
Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation.
Textual metadata on a submitted or completed job.
Textual metadata on a software author or end-user, for example a person or other software.
An informative report on a specific chemical compound.
Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on.
An informative report about a specific scent.
Data concerning or derived from a concept from a biological ontology.
Keyword(s) or phrase(s) used (typically) for text-searching purposes.
Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.
A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.
Bibliographic data that uniquely identifies a scientific article, book or other published material.
A body of scientific text, typically a full text article from a scientific journal.
A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.
An abstract of the results of text mining.
An identifier of a biological entity or phenomenon.
An identifier that identifies a particular type of data.
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
An identifier of a bioinformatics tool, e.g. an application or web service.
Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence).
Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing).
Name or other identifier of a collection of discrete biological entities.
Name or other identifier of a physical, observable biological occurrence or event.
Identifier (e.g. character symbol) of a specific atom.
A label (text token) describing the type a molecule.
For example, 'Protein', 'DNA', 'RNA' etc.
Unique identifier of a chemical compound.
Unique registry number of a chemical compound.
Code word for a ligand, for example from a PDB file.
Name or other identifier of a nucleotide.
This is the recommended chemical name for use for example in database annotation.
Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound.
IUPAC recommended name of a chemical compound.
International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO).
CAS registry number of a chemical compound.
Beilstein registry number of a chemical compound.
Gmelin registry number of a chemical compound.
3-letter code word for a ligand (HET group) from a PDB file, for example ATP.
String of one or more ASCII characters representing an amino acid.
String of one or more ASCII characters representing a nucleotide.
This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
Identifier of a polypeptide chain from a protein.
Name or other identifier of an enzyme or record from a database of enzymes.
An Enzyme Commission (EC) number of an enzyme.
A specification (partial or complete) of one or more positions or regions of a molecular sequence or map.
A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file.
A position of a single point (base or residue) in a sequence, or part of such a specification.
Specification of range(s) of sequence positions.
Name or other identifier of an nucleic acid feature.
Name or other identifier of a protein feature.
A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.
The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key.
Feature qualifiers hold information about a feature beyond that provided by the feature key and location.
Typically one of the EMBL or Swiss-Prot feature qualifiers.
A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.
Typically an EMBL or Swiss-Prot feature label.
The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications.
String of one or more ASCII characters representing a codon.
An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.
The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.
An NCBI RefSeq unique identifier of a gene.
An NCBI UniGene unique identifier of a gene.
Identifier of a gene or feature from the CGD database.
Unique identifier for a gene (or other feature) from the Ensembl database.
Identifier of an entry from the SGD database.
Identifier of a gene from the GeneDB database.
Identifier of an entry from the TIGR database.
Identifier of an gene from the TAIR database.
This is typically a character or string concatenated with a PDB identifier and a chain identifier.
Identifier of a protein structural domain.
Identifier of a protein domain (or other node) from the SCOP database.
Identifier of a protein domain from CATH.
SCOP concise classification string (sccs)
An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.
A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification.
A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.
Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229.
A code number identifying a node from the CATH database.
The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes).
The name of a species (typically a taxonomic group) of organism.
The name of a strain of an organism variant, typically a plant, virus or bacterium.
A string of characters that name or otherwise identify a resource on the Internet.
An identifier of a biological or bioinformatics database.
The name (or part of a name) of a file (of any type).
Name of an ontology of biological or bioinformatics concepts and relations.
A Life Science Identifier (LSID) - a unique identifier of some data.
LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
The name of a biological or bioinformatics database.
The name of a molecular sequence database.
The name of a file (of any type) with restricted possible values.
A file extension is the characters appearing after the final '.' in the file name.
A file base name is the file name stripped of its directory specification and extension.
An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type.
This concept is required for completeness. It should never have child concepts.
An identifier of molecular sequence(s) or entries from a molecular sequence database.
An identifier of a set of molecular sequence(s).
Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns.
Identifier of a molecular sequence alignment, for example a record from an alignment database.
Identifier of a phylogenetic distance matrix.
Identifier of a phylogenetic tree for example from a phylogenetic tree database.
A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database.
Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment).
Identifier of an entry from a database of tertiary structure alignments.
Identifier of an index of amino acid physicochemical and biochemical property data.
Identifier of a report of protein interactions from a protein interaction database (typically).
Protein secondary database record identifier
Identifier of a transcription factor (or a TF binding site).
Identifier of an entry from a database of microarray data.
Identifier of an entry from a database of electron microscopy data.
Accession of a report of gene expression (e.g. a gene expression profile) from a database.
Identifier of an entry from a database of genotypes and phenotypes.
Identifier of an entry from a database of biological pathways or networks.
Identifier of a biological or biomedical workflow, typically from a database of workflows.
Identifier of a data type definition from some provider.
Identifier of a mathematical model, typically an entry from a database.
Identifier of an entry from a database of chemicals.
A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
Unique identifier of a scientific article.
Identifier of an object from the FlyBase database.
Name of an object from the WormBase database, usually a human-readable name.
A WormBase class describes the type of object such as 'sequence' or 'protein'.
Class of an object from the WormBase database.
A persistent, unique identifier of a molecular sequence database entry.
A label (text token) describing a type of molecular sequence.
Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications.
Accession number of a protein sequence database entry.
Accession number of a nucleotide sequence database entry.
Accession number of a RefSeq database entry.
Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.
An identifier of PIR sequence database entry.
Identifier of a TREMBL sequence database entry.
Primary identifier of a Gramene database entry.
Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases.
A unique identifier of an entry (gene cluster) from the NCBI UniGene database.
The EMBOSS type of a molecular sequence.
See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.
List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile).
An identifier of a cluster of molecular sequence(s).
Unique identifier of an entry from the COG database.
Identifier of a sequence motif, for example an entry from a motif database.
A sequence profile typically represents a sequence alignment.
Identifier of an entry from the ELMdb database of protein functional sites.
Accession number of an entry from the Prosite database.
Unique identifier or name of a HMMER hidden Markov model.
Unique identifier or name of a profile from the JASPAR database.
A label (text token) describing the type of a sequence alignment.
Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
A label (text token) describing the type of a phylogenetic tree.
Accession number of an entry from the TreeBASE database.
Accession number of an entry from the TreeFam database.
For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.
A label (text token) describing the type of a comparison matrix.
Unique name or identifier of a comparison matrix.
See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
An identifier of an entry from the PDB database.
Identifier of an entry from the AAindex database.
Accession number of an entry from the BIND database.
Accession number of an entry from the IntAct database.
Name of an InterPro entry, usually indicating the type of protein matches for that entry.
Every InterPro entry has a unique accession number to provide a persistent citation of database records.
Primary accession number of an InterPro entry.
Secondary accession number of an InterPro entry.
Unique identifier of an entry from the Gene3D database.
Unique identifier of an entry from the PIRSF database.
The unique identifier of an entry in the PRINTS database.
Accession number of an entry from the SMART database.
Unique identifier (number) of a hidden Markov model from the Superfamily database.
Accession number of an entry (family) from the TIGRFam database.
ProDom is a protein domain family database.
A ProDom domain family accession number.
Identifier of an entry from the TRANSFAC database.
Accession number of an entry from the ArrayExpress database.
Identifier of an entry from the EMDB electron microscopy database.
Accession number of an entry from the GEO database.
Identifier of an entry from the GermOnline database.
Identifier of an entry from the EMAGE database.
Identifier of an entry from a database of disease.
Identifier of an entry from the HGVbase database.
Identifier of an entry from the HIVDB database.
Identifier of an entry from the OMIM database.
Unique identifier of an object from one of the KEGG databases (excluding the GENES division).
Identifier of an entry from the Reactome database.
Identifier of an entry from the aMAZE database.
Identifier of an pathway from the BioCyc biological pathways database.
Identifier of an entry from the INOH database.
Identifier of an entry from the PATIKA database.
Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB.
This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.
Identifier of a biological pathway from the Panther Pathways database.
Unique identifier of a MIRIAM data resource.
This is the identifier used internally by MIRIAM for a data type.
The name of a data type from the MIRIAM database.
A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.
The URI (URL or URN) of a data entity from the MIRIAM database.
The primary name of a data type from the MIRIAM database.
The primary name of a MIRIAM data type is taken from a controlled vocabulary.
A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'.
A synonymous name for a MIRIAM data type taken from a controlled vocabulary.
A synonymous name of a data type from the MIRIAM database.
Unique identifier of a Taverna workflow.
Name of a biological (mathematical) model.
Unique identifier of an entry from the BioModel database.
Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure.
Identifier of an entry from the ChemSpider database.
Identifier of an entry from the ChEBI database.
An identifier of a concept from the BioPax ontology.
An identifier of a concept from The Gene Ontology.
An identifier of a concept from the MeSH vocabulary.
An identifier of a concept from the HGNC controlled vocabulary.
A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database.
An identifier of a concept from the Plant Ontology (PO).
An identifier of a concept from the UMLS vocabulary.
Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
An identifier of a concept from Foundational Model of Anatomy.
An identifier of a concept from the EMAP mouse ontology.
An identifier of a concept from the ChEBI ontology.
An identifier of a concept from the MGED ontology.
An identifier of a concept from the myGrid ontology.
The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
Digital Object Identifier (DOI) of a published article.
The use of Medline UI has been replaced by the PubMed unique identifier.
Medline UI (unique identifier) of an article.
The name of a computer package, application, method or function.
Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.
The unique name of a signature (sequence classifier) method.
This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.
This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.
Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
The cluster might include sequences identifiers, short descriptions, alignment and summary information.
A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration.
A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.
Sequences generated by HMMER package in FASTA-style format.
A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses.
Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease.
Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set.
vectorstrip cloning vector definition file
File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format.
Primer3 internal oligo mishybridizing library
A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format.
A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format.
primersearch primer pairs sequence record
File of one or more pairs of primer sequences, as used by EMBOSS primersearch application.
The sequences are typically related, for example a family of sequences.
The size (length) of a sequence, subsequence or region in a sequence.
Word size is used for example in word-based sequence database search methods.
A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.
Specification of range(s) of length of sequences.
Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc.
An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.
Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.
This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.
Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc.
A report of general sequence properties derived from protein sequence data.
A report of general sequence properties derived from nucleotide sequence data.
A report on sequence complexity, for example low-complexity or repeat regions in sequences.
A report on ambiguity in molecular sequence(s).
A report (typically a table) on character or word composition / frequency of a molecular sequence(s).
A report on peptide fragments of certain molecular weight(s) in one or more protein sequences.
Sequence composition (base position variability)
Report on or plot of third base position variability in a nucleotide sequence.
A table of character or word composition / frequency of a molecular sequence.
A table of base frequencies of a nucleotide sequence.
A table of word composition of a nucleotide sequence.
A table of amino acid frequencies of a protein sequence.
Sequence composition (amino acid frequencies)
A table of amino acid word composition of a protein sequence.
Annotation of a molecular sequence in DAS format.
Annotation of positional sequence features, organized into a standard feature table.
A map of (typically one) DNA sequence annotated with positional or non-positional features.
Nucleotide sequence-specific feature annotation (positional features of a nucleotide sequence).
This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.
This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.
Protein sequence-specific feature annotation (positional features of a protein sequence).
A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.
A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.
A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs.
A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.
Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them.
Image of a sequence with matches to signatures, motifs or profiles.
This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.
A map showing banding patterns derived from direct observation of a stained chromosome.
A gene map showing distances between loci based on relative cotransduction frequencies.
Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene.
Sequence map of a plasmid (circular DNA).
Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
Image showing matches between protein sequence(s) and InterPro Entries.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.
Image showing detailed information on matches between protein sequence(s) and InterPro Entries.
Image showing the architecture of InterPro domains in a protein sequence.
The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.
Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences.
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences.
Use this concept if another, more specific concept is not available.
Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
The report might include derived data map such as classification, annotation, organization, periodicity etc.
Nucleic acid features (gene and transcript structure)
A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
Nucleic acid features (mobile genetic elements)
A report on a region of a nucleic acid sequence containin mobile genetic elements.
This includes transposons, Plasmids, Bacteriophage elements and Group II introns.
Nucleic acid features (PolyA signal or site)
A region or site in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript.
A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation.
A report on quadruplex-forming motifs in a nucleotide sequence.
Nucleic acid features (CpG island and isochore)
A report or plot of CpG rich regions (isochores) in a nucleotide sequence.
Nucleic acid features (restriction sites)
Report on restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence.
Nucleic acid features (nucleosome exclusion sequences)
A report on nucleosome formation potential or exclusion sequence(s).
A report on splice sites in a nucleotide sequence or alternative RNA splicing events.
Nucleic acid features (matrix/scaffold attachment sites)
A report on matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence.
Gene features (exonic splicing enhancer)
A report on exonic splicing enhancers (ESE) in an exon.
A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc.
A report on operons (operators, promoters and genes) from a bacterial genome.
The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query.
A report on whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence.
A report on protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames.
A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence.
A report on the transcription factor binding sites (TFBS) in a DNA sequence.
A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites.
Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.
A report on the location of signal peptides or signal peptide cleavage sites in protein sequences.
A report on cleavage sites (for a proteolytic enzyme or agent) in a protein sequence.
Protein features (post-translation modifications)
A report on post-translation modifications in a protein sequence, typically describing the specific sites involved.
Protein features (post-translation modification sites)
A report on catalytic residues (active site) of an enzyme.
A report on ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids.
Epitope mapping is commonly done during vaccine design.
A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data.
Protein features (nucleic acid binding sites)
A report on RNA and DNA-binding proteins and binding sites in protein sequences.
A report on epitopes that bind to MHC class I molecules.
A report on predicted epitopes that bind to MHC class II molecules.
'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.
A report or plot of PEST sites in a protein sequence.
Scores from a sequence database search (for example a BLAST search).
Alignments from a sequence database search (for example a BLAST search).
A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search).
Alphabet for the motifs (patterns) that MEME will search for.
File of directives for ordering and spacing of MEME motifs.
Dirichlet distribution used by hidden Markov model analysis programs.
Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states.
Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.
Some type of statistical model representing a (typically multiple) sequence alignment.
An entry (sequence classifier and associated data) from the InterPro database.
A nucleotide regular expression pattern from the Prosite database.
A protein regular expression pattern from the Prosite database.
A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position.
Contributions of individual sequences to the matrix might be uneven (weighted).
A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.
A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position.
A hidden Markov model representation of a set or alignment of sequences.
One or more fingerprints (sequence classifiers) as used in the PRINTS database.
A protein signature of the type used in the EMBASSY Signature package.
NULL hidden Markov model representation used by the HMMER package.
A protein family signature (sequence classifier) from the InterPro database.
Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.
Protein domain signatures identify structural or functional domains or other units with defined boundaries.
A protein domain signature (sequence classifier) from the InterPro database.
A protein region signature defines a region which cannot be described as a protein family or domain signature.
A protein region signature (sequence classifier) from the InterPro database.
A protein repeat signature (sequence classifier) from the InterPro database.
A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
A protein site signature (sequence classifier) from the InterPro database.
A protein site signature is a classifier for a specific site in a protein.
A protein conserved site signature (sequence classifier) from the InterPro database.
A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.
A protein active site signature (sequence classifier) from the InterPro database.
A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
A protein binding site signature (sequence classifier) from the InterPro database.
Protein post-translational modification signature
A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
A protein post-translational modification signature (sequence classifier) from the InterPro database.
Alignment of exactly two molecular sequences.
Alignment of more than two molecular sequences.
Alignment of multiple nucleotide sequences.
Alignment of multiple protein sequences.
Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.
Alignment of multiple molecular sequences of different types.
Alignment of exactly two nucleotide sequences.
Alignment of exactly two protein sequences.
Alignment of exactly two molecular sequences of different types.
Alignment of more than two nucleotide sequences.
Alignment of more than two protein sequences.
A simple floating point number defining the penalty for opening or extending a gap in an alignment.
Controls the order of sequences in an output sequence alignment.
A penalty for opening a gap in an alignment.
A penalty for extending a gap in an alignment.
A penalty for gaps that are close together in an alignment.
A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
The score for a 'match' used in various sequence database search applications with simple scoring schemes.
The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes.
This is the threshold drop in score at which extension of word alignment is halted.
A simple floating point number defining the penalty for opening a gap in an alignment.
A simple floating point number defining the penalty for extending a gap in an alignment.
A simple floating point number defining the penalty for gaps that are close together in an alignment.
A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences.
Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.
Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension.
Sequence alignment metadata (quality report)
Data on molecular sequence alignment quality (estimated accuracy).
Sequence alignment report (site conservation)
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
Data on character conservation in a molecular sequence alignment.
Sequence alignment report (site correlation)
Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures.
Sequence-profile alignment (Domainatrix signature)
Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment).
Alignment of molecular sequence(s) to a hidden Markov model(s).
Sequence-profile alignment (fingerprint)
Alignment of molecular sequences to a protein fingerprint from the PRINTS database.
Phylogenetic continuous quantitative data
Continuous quantitative data that may be read during phylogenetic tree calculation.
Phylogenetic continuous quantitative characters
Character data with discrete states that may be read during phylogenetic tree calculation.
One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny.
Phylogenetic invariants data for testing alternative tree topologies.
A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.
This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.
A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis.
Sequence alignment report (DNA substitution model)
Phylogenetic tree report (DNA substitution model)
Data about the shape of a phylogenetic tree.
Phylogenetic tree report (tree evaluation)
Data on the confidence of a phylogenetic tree.
Distances, such as Branch Score distance, between two or more phylogenetic trees.
Phylogenetic tree report (tree distances)
Phylogenetic tree report (tree stratigraphic)
Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis.
Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts.
Phylogenetic report (character contrasts)
Matrix of integer numbers for sequence comparison.
Matrix of floating point numbers for sequence comparison.
Matrix of integer or floating point numbers for nucleotide comparison.
Matrix of integer or floating point numbers for amino acid comparison.
Matrix of integer numbers for nucleotide comparison.
Nucleotide substitution matrix (integers)
Matrix of floating point numbers for nucleotide comparison.
Amino acid substitution matrix (integers)
Matrix of integer numbers for amino acid comparison.
Matrix of floating point numbers for amino acid comparison.
An informative report on trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements.
This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.
3D coordinate and associated data for a nucleic acid tertiary (3D) structure.
3D coordinate and associated data for a protein tertiary (3D) structure.
This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.
The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.
3D coordinate and associated data for a carbohydrate (3D) structure.
3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound.
3D coordinate and associated data for a DNA tertiary (3D) structure.
3D coordinate and associated data for an RNA tertiary (3D) structure.
3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc.
3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain.
3D coordinate and associated data for the tertiary (3D) structure of a protein domain.
3D coordinate and associated data for a protein tertiary (3D) structure (all atoms).
C-beta atoms from amino acid side-chains may be included.
3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only).
3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms).
3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only).
3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms).
3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only).
Alignment (superimposition) of exactly two molecular tertiary (3D) structures.
Alignment (superimposition) of more than two molecular tertiary (3D) structures.
Alignment (superimposition) of protein tertiary (3D) structures.
Alignment (superimposition) of nucleic acid tertiary (3D) structures.
Alignment (superimposition) of exactly two protein tertiary (3D) structures.
Multiple protein tertiary structure alignment
Alignment (superimposition) of more than two protein tertiary (3D) structures.
Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered).
Structure alignment (protein C-alpha atoms)
C-beta atoms from amino acid side-chains may be considered.
Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered).
Pairwise protein tertiary structure alignment (all atoms)
Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered).
Pairwise protein tertiary structure alignment (C-alpha atoms)
Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered).
Multiple protein tertiary structure alignment (all atoms)
Multiple protein tertiary structure alignment (C-alpha atoms)
Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures.
Multiple nucleic acid tertiary structure alignment
Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures.
Alignment (superimposition) of RNA tertiary (3D) structures.
Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures.
The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.
DaliLite hit table of protein chain tertiary structure alignment data.
A score reflecting structural similarities of two molecules.
Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates.
A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.
A measure of the similarity between two ligand fingerprints.
A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments.
A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids.
Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids.
Hydrophobic, hydrophilic or charge properties of amino acids.
Experimental free energy values for the water-interface and water-octanol transitions for the amino acids.
Van der Waals radii of atoms for different amino acid residues.
An informative report on a specific enzyme.
This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
An informative report on a specific restriction enzyme such as enzyme reference data.
The report might include associated data such as frequency of peptide fragment molecular weights.
List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents.
Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
Report on the hydrophobic moment of a polypeptide sequence.
The aliphatic index is the relative protein volume occupied by aliphatic side chains.
A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc.
A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence.
The solubility or atomic solvation energy of a protein sequence or structure.
Data on the crystallizability of a protein sequence.
Data on the stability, intrinsic disorder or globularity of a protein sequence.
The hydrogen exchange rate of a protein.
The extinction coefficient of a protein.
An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins).
Protein report (subcellular localization)
This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
An report on allergenicity / immunogenicity of peptides and proteins.
A report on the immunogenicity of MHC class I or class II binding peptides.
Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains.
This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).
Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.
Protein structure report (quality evaluation)
Report on the quality of a protein three-dimensional model.
Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups.
Protein structure report (flexibility or motion)
Informative report on flexibility or motion of a protein structure.
Protein property (flexibility or motion)
Data on the solvent accessible or buried surface area of a protein structure.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.
Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure.
Phi/psi angle data or a Ramachandran plot of a protein structure.
Data on the net charge distribution (dipole moment) of a protein structure.
A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure.
An amino acid residue contact map for a protein structure.
Report on clusters of contacting residues in protein structures such as a key structural residue network.
Patterns of hydrogen bonding in protein structures.
Non-canonical atomic interactions in protein structures.
Protein non-canonical interactions report
Information on a node from the CATH database.
The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.
Information on a node from the SCOP database.
An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format.
Information on a protein 'class' node from the CATH database.
Information on a protein 'architecture' node from the CATH database.
Information on a protein 'topology' node from the CATH database.
Information on a protein 'homologous superfamily' node from the CATH database.
Information on a protein 'structurally similar group' node from the CATH database.
Information on a protein 'functional category' node from the CATH database.
A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s).
Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
For example, an informative report about a specific protein complex (of multiple polypeptide chains).
Protein structure report (protein complex)
Data on protein-ligand (small molecule) interaction(s).
Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.
A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.
Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).
Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA).
Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA).
A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature.
Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA).
RNA parameters used by the Vienna package.
Structure constraints used by the Vienna package.
RNA concentration data used by the Vienna package.
RNA calculated energy data generated by the Vienna package.
Dotplot of RNA base pairing probability matrix.
Such as generated by the Vienna package.
A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.
A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.
Table of codon usage data calculated from one or more nucleic acid sequences.
A genetic code need not include detailed codon usage information.
A simple measure of synonymous codon usage bias often used to predict gene expression levels.
A plot of the synonymous codon usage calculated for windows over a nucleotide sequence.
The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons.
The differences in codon usage fractions between two codon usage tables.
Data on the influence of genotype on drug response.
The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.
An informative report on a specific disease.
Gene annotation (linkage disequilibrium)
A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context.
A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment.
Affymetrix library file of information about which probes belong to which probe set.
Affymetrix probe sets information library file
Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated.
Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS.
A report typically including a map (diagram) of a metabolic pathway.
This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
Pathway or network (genetic information processing)
A report typically including a map (diagram) of a genetic information processing pathway.
Pathway or network (environmental information processing)
A report typically including a map (diagram) of an environmental information processing pathway.
Pathway or network (signal transduction)
A report typically including a map (diagram) of a signal transduction pathway.
A report typically including a map (diagram) of a cellular process pathway.
A report typically including a map (diagram) of a disease pathway, typically a diagram for a human disease.
Pathway or network (drug structure relationship)
A report typically including a map (diagram) of drug structure relationships.
Pathway or network (protein-protein interaction)
A report typically including a map (diagram) of a network of protein interactions.
An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.
A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
A simple floating point number defining the lower or upper limit of an expectation value (E-value).
An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.
A z-value might be specified as a threshold for reporting hits from database searches.
The z-value is the number of standard deviations a data value is above or below a mean value.
The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true.
Information on a database (or ontology) version, for example name, version number and release date.
Information on an application version, for example name, version number and release date.
Information on a version of the CATH database.
Cross-mapping of Swiss-Prot codes to PDB identifiers.
Cross-references from a sequence record to other databases.
Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
Metadata on the status of a submitted job.
The (typically numeric) unique identifier of a submitted job.
A label (text token) describing the type of job, for example interactive or non-interactive.
A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages.
DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures.
EMBOSS (EMBASSY) domainatrix application log file.
EMBOSS (EMBASSY) sites application log file.
EMBOSS (EMBASSY) supermatcher error file.
Number of entities (for example database hits, sequences, alignments etc) to write to an output file.
Controls the order of hits (reported matches) in an output file from a database search.
An informative report on a specific drug.
An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information.
Image of RNA secondary structure, knots, pseudoknots etc.
Image of one or more molecular tertiary (3D) structures.
Image of two or more aligned molecular sequences possibly annotated with alignment features.
The molecular identifier and formula are typically included.
An image of the structure of a small chemical compound.
A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development.
An image of spots from a microarray experiment.
A term definition from The Gene Ontology (GO).
A term from the HGNC controlled vocabulary.
A term from the NCBI taxonomy vocabulary.
A term from Foundational Model of Anatomy.
A term definition for a biological process from the Gene Ontology (GO).
A term definition for a molecular function from the Gene Ontology (GO).
A term definition for a cellular component from the Gene Ontology (GO).
The definition of a concept from an ontology.
A comment on a concept from an ontology.
Reference for a concept from an ontology.
Information on a published article provided by the doc2loc program.
The doc2loc output includes the url, format, type and availability code of a document for every service provider.
A residue identifier (a string) from a PDB file.
Cartesian coordinate of an atom (in a molecular structure).
Cartesian x coordinate of an atom (in a molecular structure).
Cartesian y coordinate of an atom (in a molecular structure).
Cartesian z coordinate of an atom (in a molecular structure).
Identifier (a string) of a specific atom from a PDB file for a molecular structure.
Data on a single atom from a protein structure.
Data on a single amino acid residue position in a protein structure.
Three-letter amino acid residue names as used in PDB files.
Identifier of a model structure from a PDB file.
The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
Summary of domain classification information for a CATH domain.
CATH representative domain sequences (ATOM)
FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity).
CATH representative domain sequences (COMBS)
FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity).
FASTA sequence database for all CATH domains (based on PDB ATOM records).
FASTA sequence database for all CATH domains (based on COMBS sequence data).
Information on an molecular sequence version.
A numerical value, either some type of scored value arising for example from a prediction method or a value used in a scoring scheme, which might reduce the final score (penalty).
Report on general functional properties of specific protein(s).
For properties that can be mapped to a sequence, use 'Sequence report' instead.
Name of a gene from Aspergillus Genome Database.
Name of a gene from Candida Genome Database.
Primary name of a gene from EcoGene Database.
Name of a gene from MaizeGDB (maize genes) database.
Name of a gene from Saccharomyces Genome Database.
Name of a gene from Tetrahymena Genome Database.
Symbol of a gene from E.coli Genetic Stock Center.
http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
Symbol of a gene approved by the HUGO Gene Nomenclature Committee.
http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
http://www.geneontology.org/doc/GO.xrf_abbs: MGD
Symbol of a gene from the Mouse Genome Database.
Symbol of a gene from Bacillus subtilis Genome Sequence Project.
http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
Identifier of a gene from PlasmoDB Plasmodium Genome Resource.
Identifier of a gene from EcoGene Database.
http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
http://www.geneontology.org/doc/GO.xrf_abbs: FB
Gene identifier from Glossina morsitans GeneDB database.
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor
Gene identifier from Leishmania major GeneDB database.
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
Gene identifier from Plasmodium falciparum GeneDB database.
Gene ID (GeneDB Schizosaccharomyces pombe)
Gene identifier from Schizosaccharomyces pombe GeneDB database.
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
Gene identifier from Trypanosoma brucei GeneDB database.
http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
http://www.geneontology.org/doc/GO.xrf_abbs: VMD
Gene identifier from Virginia Bioinformatics Institute microbial database.
http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
Gene identifier from Sol Genomics Network.
http://www.geneontology.org/doc/GO.xrf_abbs: SGN
http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
Gene identifier used by WormBase database.
http://www.geneontology.org/doc/GO.xrf_abbs: WB
Any name (other than the recommended one) for a gene.
The name of an open reading frame attributed by a sequencing project.
A component of a larger sequence assembly.
A report on a chromosome aberration such as abnormalities in chromosome structure.
An identifier of a clone (cloned molecular sequence) from a database.
An insertion code (part of the residue number) for an amino acid residue from a PDB file.
The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.
The fraction of an atom type present at a site in a molecular structure.
Isotropic B factor (atomic displacement parameter) for an atom from a PDB file.
A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.
A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.
A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers.
A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.
Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped.
Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
A feature which may mapped (positioned) on a genetic or other type of map.
Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
A designation of the type of map (genetic map, physical map, sequence map etc) or map set.
The name of a group of organisms belonging to the same taxonomic rank.
For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
A unique identifier of a (group of) organisms.
Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.
The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.
A unique identifier for an organism used in the iHOP database.
Common name for an organism as used in the GenBank database.
The name of a taxon from the NCBI taxonomy database.
A term which is likely to be misleading of its meaning.
Information on the authors of a published work.
An identifier representing an author in the DragonDB database.
A URI along with annotation describing the data found at the address.
A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database.
Identifier of a gene from the GeneFarm database.
Identifier for genetic elements in MIPS Maize database.
Identifier for genetic elements in MIPS Medicago database.
MIPS genetic element identifier (Medicago)
The name of an Antirrhinum Gene from the DragonDB database.
A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name.
A unique identifier of a protein or gene used in the iHOP database.
Name of a gene from the GeneFarm database.
A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.
Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)
Identifier for loci from ASPGD (Aspergillus Genome Database).
http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
Identifier for loci from Magnaporthe grisea Database at the Broad Institute.
http://www.geneontology.org/doc/GO.xrf_abbs: CGD
http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
Identifier for loci from CGD (Candida Genome Database).
http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute.
http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
Identifier for loci from SGD (Saccharomyces Genome Database).
http://www.geneontology.org/doc/GO.xrf_abbs: SGD
http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
Identifier of loci from Maize Mapping Project.
Identifier of locus from DictyBase (Dictyostelium discoideum).
Identifier of a locus from EntrezGene database.
Identifier of locus from MaizeGDB (Maize genome database).
A QTL sometimes but does not necessarily correspond to a gene.
A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment).
Identifier of a gene from the KOME database.
Identifier of a locus from the Tropgene database.
An alignment of molecular sequences, structures or profiles derived from them.
Data for an atom (in a molecular structure).
http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW
A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database.
A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome.
This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.
A position in a map (for example a genetic map), either a single position (point) or a region / interval.
Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids.
A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.
An attribute of a molecular map (genetic or physical).
Data used by the Vienna RNA analysis package.
Data used to replace (mask) characters in a molecular sequence.
Data concerning chemical reaction(s) catalysed by enzyme(s).
A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent.
A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v).
Raw data from or annotation on laboratory experiments.
Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc.
A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
One or more molecular sequences, possibly with associated annotation.
This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment.
This is a broad data type and is used a placeholder for other, more specific types. The notions of 'data', 'report', 'annotation' and 'metadata' are somewhat subjective and overlapping. 'Report' is used to indicate human-readable collections of information which (typically) are computer-generated from analysis of primary (e.g. core sequence or structural) data, as distinct from the primary data itself or human-generated annotation on an entity. 'Annotation' indicates human-readable collections of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. 'Metadata' indicates data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing.
A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary (e.g. sequence or structural) data, metadata about the primary data, and any free (essentially unformatted) text, as distinct from the primary data itself.
Data concerning molecular structural data.
Some simple value controlling a search operation, typically a search of a database.
A report of hits from searching a database of some type.
The secondary structure assignment (predicted or real) of a nucleic acid or protein.
An array of numerical values where (typically) the rows and columns correspond to molecular entities and the values are comparative data, for example, distances between molecular sequences.
An informative report about a molecular alignment of some type, including alignment-derived data or metadata.
An informative report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data.
An informative report on general information, properties or features of one or more molecular tertiary (3D) structures.
A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s).
This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties.
A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.
Structural data for DNA base pairs or runs of bases, such as energy or angle data.
Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on.
A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.
An SNP is an individual point mutation or substitution of a single nucleotide.
Annotation on a single nucleotide polymorphism (SNP) in a DNA sequence.
Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.
A list of database accessions or identifiers are usually included.
A name of a thing, which need not necessarily uniquely identify it.
Closely related, but focusing on labeling and human readability but not on identification.
A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values).
An identifier of a software end-user (typically a person).
A three-letter code used in the KEGG databases to uniquely identify organisms.
Name of an entry (gene) from the KEGG GENES database.
Identifier of an object from one of the BioCyc databases.
Identifier of a compound from the BioCyc chemical compounds database.
Identifier of a biological reaction from the BioCyc reactions database.
Identifier of an enzyme from the BioCyc enzymes database.
Identifier of a biological reaction from a database.
This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
An identifier that is re-used for data objects of fundamentally different types (typically served from a single database).
Identifier of a codon usage table, for example a genetic code.
Primary identifier of an object from the FlyBase database.
Identifier of an object from the WormBase database.
Protein identifier used by WormBase database.
An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon.
An identifier of a map of a molecular sequence.
Name or other identifier of a nucleic acid molecule.
Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome).
Informal name for a genetic code, typically an organism name.
Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.
A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc.
Name of a computer operating system such as Linux, PC or Mac.
A type of point or block mutation, including insertion, deletion, change, duplication and moves.
A logical operator such as OR, AND, XOR, and NOT.
A control of the order of data that is output, for example the order of sequences in an alignment.
Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.
A simple parameter that is a toggle (boolean value), typically a control for a modal tool.
The width of an output sequence or alignment.
A penalty for introducing or extending a gap in an alignment.
A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate.
The concentration of a chemical compound.
Size of the incremental 'step' a sequence window is moved over a sequence.
An image of a graph generated by the EMBOSS suite.
An application report generated by the EMBOSS suite.
An offset for a single-point sequence position.
A value that serves as a threshold for a tool (usually to control scoring or output).
An informative report on a transcription factor protein.
This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
The name of a category of biological or bioinformatics database.
A parameter that is used to control rendering (drawing) to a device or image.
Any arbitrary name of a molecular sequence.
Word composition data for a molecular sequence.
A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences.
A plot of sequence similarities identified from word-matching or character comparison.
Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties.
An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix.
Useful for highlighting amphipathicity and other properties.
A plot of general physicochemical properties of a protein sequence.
A plot of character or word composition / frequency of a molecular sequence.
Density plot (of base composition) for a nucleotide sequence.
Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases).
A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing.
This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.
Secondary identifier are used to handle entries that were merged with or split from other entries in the database.
Secondary identifier of an object from the FlyBase database.
A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing.
Protein features (chemical modification)
A report on a chemical modification of a protein.
Data on an error generated by computer system or tool.
Basic information on any arbitrary database entry.
A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
An identifier of a plasmid in a database.
A unique identifier of a specific mutation catalogued in a database.
Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style.
An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type)..
An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study.
An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on.
The number of a codon, for instance, at which a mutation is located.
An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.
Basic information about a server on the web, such as an SRS server.
Unique identifier of a sequence cluster from the SYSTERS database.
These are the parsable data files provided by SCOP.
Raw SCOP domain classification data files.
These are the parsable data files provided by CATH.
Raw CATH domain classification data files.
An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files.
A collection of sequences output from a bootstrapping (resampling) procedure.
Bootstrapping is often performed in phylogenetic analysis.
A consensus phylogenetic tree derived from comparison of multiple trees.
A data schema for organising or transforming data of some type.
Name of an OBO file format such as OBO-XML, plain and so on.
Identifier for genetic elements in MIPS database.
An identifier of protein sequence(s) or protein sequence database entries.
An identifier of nucleotide sequence(s) or nucleotide sequence database entries.
An accession number of an entry from the EMBL sequence database.
An identifier of a polypeptide in the UniProt database.
Accession number of an entry from the GenBank sequence database.
Secondary (internal) identifier of a Gramene database entry.
An identifier of an entry from a database of molecular sequence variation.
A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.
Name of an entry (gene) from the AceView genes database.
http://www.geneontology.org/doc/GO.xrf_abbs: ECK
Identifier of an E. coli K-12 gene from EcoGene Database.
Identifier for a gene approved by the HUGO Gene Nomenclature Committee.
The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol.
Name of an entry (gene) from the NCBI genes database.
A specification of a chemical structure in SMILES format.
Unique identifier of an entry from the STRING database of protein-protein interactions.
An informative report on a specific virus.
An informative report on the taxonomy of a specific virus.
Identifier of a biological reaction from the SABIO-RK reactions database.
Annotation on or information derived from one or more specific carbohydrate 3D structure(s).
Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.
Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.
An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.
A unique, persistent identifier of an enzyme.
Identifier of an enzyme from the REBASE enzymes database.
Unique identifier of a drug from the DrugBank database.
A unique identifier assigned to NCBI protein sequence records.
Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches.
A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system.
Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence.
Data concerning or describing some core data, as distinct from the primary data that is being described. This includes metadata on the origin, source, history, ownership or location of some thing.
Any arbitrary identifier of an ontology.
An identifier of a build of a particular genome.
The name of a biological pathway or network.
Identifier of a pathway from the KEGG pathway database.
Identifier of a pathway from the NCI-Nature pathway database.
Identifier of a pathway from the ConsensusPathDB pathway database.
Unique identifier of an entry from the UniRef database.
Unique identifier of an entry from the UniRef100 database.
Unique identifier of an entry from the UniRef90 database.
Unique identifier of an entry from the UniRef50 database.
An informative report on a specific RNA family or other group of classified RNA sequences.
Identifier of an RNA family, typically an entry from a RNA sequence classification database.
Stable accession number of an entry (RNA family) from the RFAM database.
A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database.
Data on protein domain-DNA/RNA interaction(s).
Data on protein domain-protein domain interaction(s).
Data on indirect protein domain-protein domain interaction(s).
Accession number of a nucleotide or protein sequence database entry.
Data concerning two-dimensional polygel electrophoresis.
An informative report on a two-dimensional gel electrophoresis experiment, gel or spots in a gel.
A persistent, unique identifier of a biological pathway or network (typically a database entry).
Alignment of the (1D representations of) secondary structure of two or more molecules.
Identifier of an object from the ASTD database.
Identifier of an exon from the ASTD database.
Identifier of an intron from the ASTD database.
Identifier of a polyA signal from the ASTD database.
Identifier of a transcription start site from the ASTD database.
An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel.
Unique identifier of a spot from a two-dimensional (protein) gel.
Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database.
Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database.
Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs.
Identifier of a strain of an organism variant, typically a plant, virus or bacterium.
A unique identifier of an item from the CABRI database.
Metadata on a genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods.
Identifier of an entry from a database of genotype experiment metadata.
Identifier of an entry from the EGA database.
Identifier of a protein entry catalogued in the International Protein Index (IPI) database.
Accession number of a protein from the RefSeq database.
Identifier of an entry (promoter) from the EPD database.
Identifier of an entry from the TAIR database.
Identifier of an Arabidopsis thaliana gene from the TAIR database.
Identifier of an entry from the UniSTS database.
Identifier of an entry from the UNITE database.
Identifier of an entry from the UTR database.
Accession number of a UniParc (protein sequence) database entry.
Identifier of an entry from the Rouge or HUGE databases.
An informative report on a specific fungus.
An informative report on a specific fungus anamorph.
An informative report on an exon in a nucleotide sequences.
Unique identifier for a protein from the Ensembl database.
An informative report on a specific gene transcript, clone or EST.
An informative report on a specific toxin.
An informative report on a membrane protein.
Informative report on protein-drug interaction(s) including binding affinity data.
Data concerning a map of molecular sequence(s).
Data concerning phylogeny, typically of molecular sequences.
Data concerning one or more protein molecules.
Data concerning one or more nucleic acid molecules.
Data concerning the scientific literature.
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.
Typically a simple numerical or string value that controls the operation of a tool.
Slightly narrower in the sense of changing the characteristics of a system/function.
Data concerning a specific type of molecule.
An informative report on a specific molecule.
An informative report on a specific organism.
Annotation on a wet lab experiment, such as experimental conditions.
A parameter concerning calculations on molecular sequences.
Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed.
SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
Data concerning a mass spectrometry measurement.
Raw data from experimental methods for determining protein structure.
Data concerning an alignment of two or more molecular sequences, structures or derived data.
This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles.
Single letter amino acid identifier, e.g. G.
Three letter amino acid identifier, e.g. GLY.
Full name of an amino acid, e.g. Glycine.
Unique identifier of a toxin from the ArachnoServer database.
Unique identifier of a monomer from the BindingDB database.
The name of a concept from the GO ontology.
An identifier of a 'biological process' concept from the the Gene Ontology.
An identifier of a 'molecular function' concept from the the Gene Ontology.
The name of a concept for a cellular component from the GO ontology.
An image arising from a Northern Blot experiment.
Unique identifier of a blot from a Northern Blot.
Unique identifier of a blot from a Northern Blot from the BlotBase database.
A biological hierarchy which might include data describing the hierarchy proper, hierarchy components and associated annotation.
Identifier of an entry from a database of biological hierarchies.
Identifier of an entry from the Brite database of biological hierarchies.
A type (represented as a string) of cancer.
A unique identifier for an organism used in the BRENDA database.
The name of a taxon using the controlled vocabulary of the UniGene database.
The name of a taxon using the controlled vocabulary of the UTRdb database.
An identifier of a catalogue of biological resources.
The name of a catalogue of biological resources from the CABRI database.
Physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules).
Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).
Data concerning one or more small molecules.
Data concerning a particular genotype, phenotype or a genotype / phenotype relation.
This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931
Image or hybridisation data for a microarray, typically a study of gene expression.
Unique identifier of a chemical compound from the KEGG database.
Name (not necessarily stable) an entry (RNA family) from the RFAM database.
Identifier of a biological reaction from the KEGG reactions database.
Unique identifier of a drug from the KEGG Drug database.
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database.
An identifier of a disease from the International Classification of Diseases (ICD) database.
Unique identifier of a sequence cluster from the CluSTr database.
Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND).
A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins.
Unique identifier of an entry from the MINT database of protein-protein interactions.
Unique identifier of an entry from the DIP database of protein-protein interactions.
Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database.
Identifier of a protein modification catalogued in a database.
Identifier of a protein modification catalogued in the RESID database.
Identifier of an entry from the RGD database.
Identifier of a protein sequence from the TAIR database.
Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB).
Identifier of an entry from the LIPID MAPS database.
Identifier of a peptide from the PeptideAtlas peptide databases.
Identifier of a report of molecular interactions from a database (typically).
A unique identifier of an interaction from the BioGRID database.
Unique identifier of a peptidase enzyme from the MEROPS database.
An identifier of a mobile genetic element.
An identifier of a mobile genetic element from the Aclame database.
Identifier of an entry from the Saccharomyces genome database (SGD).
The International Standard Book Number (ISBN) is for identifying printed books.
Identifier of a metabolite from the 3DMET database.
A unique identifier of an interaction from the MatrixDB database.
A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database.
These identifiers are unique within the cPath database, however, they are not stable between releases.
Identifier of an assay from the PubChem database.
Identifier of an entry from the PubChem database.
Identifier of an enzyme reaction mechanism from the MACie database.
Identifier for a gene from the miRBase database.
Identifier for a gene from the Zebrafish information network genome (ZFIN) database.
Identifier of an enzyme-catalysed reaction from the Rhea database.
Identifier of a biological pathway from the Unipathway database.
Identifier of a small molecular from the ChEMBL database.
Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database.
Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database.
Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB).
Identifier of a drug from the Therapeutic Target Database (TTD).
Identifier of a target protein from the Therapeutic Target Database (TTD).
A unique identifier of a type or group of cells.
A unique identifier of a neuron from the NeuronDB database.
A unique identifier of a neuron from the NeuroMorpho database.
Identifier of a chemical from the ChemIDplus database.
Identifier of a pathway from the Small Molecule Pathway Database (SMPDB).
Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology.
Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database.
Identifier of an entry from the GlycomeDB database.
Identifier of an entry from the LipidBank database.
Identifier of a conserved domain from the Conserved Domain Database.
An identifier of an entry from the MMDB database.
Unique identifier of an entry from the iRefIndex database of protein-protein interactions.
Unique identifier of an entry from the ModelDB database.
Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division).
Ensembl ID ('Spermophilus tridecemlineatus')
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division).
Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division).
Identifier of a protein domain (or other node) from the CATH database.
A code number identifying a family from the CATH database.
Identifier of an enzyme from the CAZy enzymes database.
A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence).
GO concept identifier (cellular compartment)
An identifier of a 'cellular compartment' concept from the Gene Ontology.
Name of a chromosome as used in the BioCyc database.
An identifier of a gene expression profile from the CleanEx database.
An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.
Provenance metadata or other general information concerning a genome as a whole.
Unique identifier for a protein complex from the CORUM database.
Unique identifier of a position-specific scoring matrix from the CDD database.
Unique identifier for a protein from the CuticleDB database.
Identifier of a predicted transcription factor from the DBD database.
General annotation on an oligonucleotide probe.
Identifier of an oligonucleotide from a database.
Identifier of an oligonucleotide probe from the dbProbe database.
Physicochemical property data for one or more dinucleotides.
Identifier of an dinucleotide property from the DiProDB database.
Protein structure report (disordered structure)
An informative report about disordered structure in a protein.
Unique identifier for a protein from the DisProt database.
Annotation on an embryo or concerning embryological development.
Unique identifier for a gene transcript from the Ensembl database.
An informative report on one or more small molecules that are enzyme inhibitors.
An identifier of a promoter of a gene that is catalogued in a database.
Identifier of an EST sequence from the COGEME database.
A unisequence is a single sequence assembled from ESTs.
Identifier of a unisequence from the COGEME database.
This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".
A feature identifier as used in the SwissRegulon database.
A unique identifier of gene in the NMPDR database.
A FIG ID consists of four parts: a prefix, genome id, locus type and id number.
A unique identifier of gene in the Xenbase database.
A unique identifier of gene in the Genolist database.
Name of an entry (gene) from the Genolist genes database.
Identifier of an entry (promoter) from the ABS database.
Identifier of a transcription factor from the AraC-XylS database.
Name of an entry (gene) from the HUGO database.
Identifier of a locus from the PseudoCAP database.
Identifier of a locus from the UTR database.
Unique identifier of a monosaccharide from the MonosaccharideDB database.
The name of a subdivision of the Collagen Mutation Database (CMD) database.
The name of a subdivision of the Osteogenesis database.
Identifier of an entry from the GlycosciencesDB database.
A conformational energy map of the glycosidic linkages in a carbohydrate molecule.
An informative report on an intron in a nucleotide sequences.
Identifier of a membrane transport proteins from the transport classification database (TCDB).
Name of a domain from the Pfam database.
Identifier for a gene from the VectorBase database.
Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs.
Annotation on a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc.
An informative report on a particular locus.
Official name of a protein as used in the UniProt database.
The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.
One or more terms from one or more controlled vocabularies which are annotations on an entity.
Name of a protein family from the HAMAP database.
Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance.
Identifier of an RNA transcript from the H-InvDB database.
A unique identifier of gene cluster in the H-InvDB database.
Identifier of a antibody from the HPA database.
Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database.
A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI).
Identifier of a physical entity from the ConsensusPathDB database.
Name of a physical entity from the ConsensusPathDB database.
The number of a strain of algae and protozoa from the CCAP database.
An identifier of stock from a catalogue of biological resources.
A stock number from The Arabidopsis information resource (TAIR).
Identifier of an entry from the RNA editing database (REDIdb).
Name of a domain from the SMART database.
Accession number of an entry (family) from the PANTHER database.
A unique identifier for a virus from the RNAVirusDB database.
Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
An accession of annotation on a (group of) viruses (catalogued in a database).
An identifier of a genome project assigned by NCBI.
A unique identifier of a whole genome assigned by the NCBI.
Annotation on a sequence profile such as its name, length, technical details about the profile or it's construction, the biological role or annotation and so on.
Unique identifier for a membrane protein from the TopDB database.
Identifier of a two-dimensional (protein) gel.
Name of a reference map gel from the SWISS-2DPAGE database.
Unique identifier for a peroxidase protein from the PeroxiBase database.
Identifier of an entry from the SISYPHUS database of tertiary structure alignments.
Accession of an open reading frame (catalogued in a database).
Unique identifier for a ligand-gated ion channel protein from the LGICdb database.
Identifier of an EST sequence from the MaizeDB database.
A unique identifier of gene in the MfunGD database.
An identifier of a disease from the Orpha database.
Unique identifier for a protein from the EcID database.
A unique identifier of a cDNA molecule catalogued in the RefSeq database.
Unique identifier for a cone snail toxin protein from the ConoServer database.
A web site providing data (web pages) on a common theme to a HTTP client.
Identifier for a gene from the VBASE2 database.
A unique identifier for a virus from the DPVweb database.
Identifier of a pathway from the BioSystems pathway database.
Data concerning a proteomics experiment.
3D coordinate and associated data for a lipid structure.
3D coordinate and associated data for the (3D) structure of a drug.
3D coordinate and associated data for the (3D) structure of a toxin.
A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment.
A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity.
Distances (values representing similarity) between a group of molecular structures.
Bibliographic data concerning scientific article(s).
This includes any fields from the concept definition such as concept name, definition, comments and so on.
A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences.
General annotation on a Northern Blot experiment.
VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times.
Variable number of tandem repeat polymorphism
Annotation on a variable number of tandem repeat (VNTR) polymorphism in a DNA sequence.
A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.
Annotation on a microsatellite polymorphism in a DNA sequence.
Annotation on a restriction fragment length polymorphisms (RFLP) in a DNA sequence.
An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme.
A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome.
The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.
A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.
Gene frequencies data that may be read during phylogenetic tree calculation.
A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
An entry (resource) from the DRCAT bioinformatics resource catalogue.
3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.
3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role.
Annotation on or information derived from one or more specific lipid 3D structure(s).
Image of one or more molecular secondary structures.
An informative report on general information, properties or features of one or more molecular secondary structures.
DNA sequence-specific feature annotation (not in a feature table).
Features concerning RNA or regions of DNA that encode an RNA molecule.
Biological data that is plotted as a graph of some type.
Nucleic acid features (polymorphism annotation)
A protein sequence and associated metadata.
A nucleic acid sequence and associated metadata.
A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database.
Accession of a mathematical model, typically an entry from a database.
Accession of a type or group of cells (catalogued in a database).
Accession of an entry from a database of chemicals.
Accession of a toxin (catalogued in a database).
Accession of a monosaccharide (catalogued in a database).
Accession of an entry from a database of carbohydrates.
Accession of a specific molecule (catalogued in a database).
Accession of a data definition (catalogued in a database).
An accession of a particular genome (in a database).
An accession of a map of a molecular sequence (deposited in a database).
Accession of an entry from a database of lipids.
Accession of a peptide deposited in a database.
Accession of a protein deposited in a database.
An accession of annotation on a (group of) organisms (catalogued in a database).
The name of an organism (or group of organisms).
Accession of a protein family (that is deposited in a database).
Accession of an entry from a database of transcription factors or binding sites.
An identifier of an entry from the DDBJ sequence database.
An identifier of an entity from the ConsensusPathDB database.
Data concerning or derived from the analysis of a scientific article.
An informative report derived from molecular sequence analysis, including annotation on positional features (such as a feature table) or non-positional properties, and reports of general information (metadata).
An informative report about the properties or features of one or more protein secondary structures.
A Hopp and Woods plot of predicted antigenicity of a peptide or protein.
A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Shows the proportion of nucleic acid which are double-stranded versus temperature.
Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature
A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
Plots melting temperature versus base position.
A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA).
A report typically including a map (diagram) of a gene regulatory network.
An informative report on a two-dimensional (2D PAGE) gel.
General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set.
An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data.
Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type.
Image of a molecular sequence, possibly with sequence features or properties shown.
A report on protein properties concerning hydropathy.
Data concerning a computational workflow.
Data concerning molecular secondary structure data.
A raw protein sequence (string of characters).
One or more protein sequences, possibly with associated annotation.
One or more nucleic acid sequences, possibly with associated annotation.
Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.
Data concerning the classification of protein sequences or structures.
Data concerning specific or conserved pattern in molecular sequences.
Data concerning models representing a (typically multiple) sequence alignment.
Data concerning a specific biological pathway or network.
An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.
A thermodynamic or kinetic property of a nucleic acid molecule.
Nucleic acid property (thermodynamic or kinetic)
Data concerning the classification of nucleic acid sequences or structures.
Data concerning a classification of molecular sequences, structures or other entities.
This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
A report on key residues involved in protein folding.
Torsion angle data for a protein structure.
Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted.
Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.
Accession number of a UniProt (protein sequence) database entry.
Identifier of a genetic code in the NCBI list of genetic codes.
Identifier of a concept in an ontology of biological or bioinformatics concepts and relations.
The name of a concept for a biological process from the GO ontology.
The name of a concept for a molecular function from the GO ontology.
Data concerning the classification, identification and naming of organisms.
This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.
EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.
Core data entities typically have a format and may be identified by an accession number.
Name or other identifier of molecular sequence feature(s).
An identifier of a molecular tertiary structure, typically an entry from a structure database.
An identifier of an array of numerical values, such as a comparison matrix.
A report (typically a table) on character or word composition / frequency of protein sequence(s).
A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s).
Sequence property (nucleic acid composition)
A node from a classification of protein structural domain(s).
Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service.
Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC).
A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA).
Basic information concerning geographical location or time.
Metadata concerning the software, hardware or other aspects of a computer system.
A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user.
Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.
Such data as found in Affymetrix CEL or GPR files.
Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment.
Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.
Data generated from processing and analysis of probe set data from a microarray experiment.
The final processed (normalised) data for a set of hybridisations in a microarray experiment.
This combines data from all hybridisations.
This might include compound and dose in a dose response experiment.
Annotation on a biological sample, for example experimental factors and their values.
Annotation on the array itself used in a microarray experiment.
This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.
Annotation on laboratory and/or data processing protocols used in an microarray experiment.
This might describe e.g. the normalisation methods used to process the raw data.
Data concerning the hybridisations measured during a microarray experiment.
Summary of topological domains such as cytoplasmic regions in a protein.
Sequence features (compositionally-biased regions)
A report of regions in a molecular sequence that are biased to certain characters.
A report on the protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
Nucleic acid features (difference and change)
A report on features in a nucleic acid sequence that indicate changes to or differences between sequences.
Nucleic acid features (expression signal)
A report on regions within a nucleic acid sequence containing a signal that alters a biological function.
A report on regions of a nucleic acid sequence that bind some other molecule.
This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes).
A report on repetitive elements within a nucleic acid sequence.
This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit.
Nucleic acid features (replication and recombination)
This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination.
A report on regions within a nucleic acid sequence that are involved in DNA replcication or recombination.
A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.
Location of short repetitive subsequences (repeat sequences) in a protein sequence.
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences.
Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences.
A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
A report on displacement loops in a mitochondrial DNA sequence.
A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.
A report on stem loops in a DNA sequence.
Features concerning messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.
This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
Nucleic acid features (signal or transit peptide)
A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
A report on a coding sequence for a signal or transit peptide.
Features concerning non-coding or functional RNA molecules, including tRNA and rRNA.
Features concerning transcription of DNA into RNA including the regulation of transcription.
This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
A report on sequence tagged sites (STS) in nucleic acid sequences.
Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.
Nucleic acid features (immunoglobulin gene structure)
A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments.
Information on a 'class' node from the SCOP database.
Information on a 'fold' node from the SCOP database.
Information on a 'superfamily' node from the SCOP database.
Information on a 'family' node from the SCOP database.
Information on a 'protein' node from the SCOP database.
Information on a 'species' node from the SCOP database.
Experiment annotation (mass spectrometry)
General annotation on a mass spectrometry experiment.
An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene.
An alignment of protein sequences and/or structures.
Data on a sequencing experiment, including samples, sampling, preparation, sequencing, and analysis.
This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.
An informative report about a DNA sequence assembly.
Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
Experiment annotation (genome-wide association study)
Metadata on a genome-wide association study (GWAS).
Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.
The position of a cytogenetic band in a genome.
Mathematical model of a network, that contains biochemical kinetics.
A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory.
An informative report on gene homologues between species.
Unique identifier for a gene tree from the Ensembl database.
A phylogenetic tree that is an estimate of the character's phylogeny.
A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled.
Name or other identifier of an entry from a biosample database.
Identifier of an object from the MGI database.
Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.
A HMM transition matrix contains the probabilities of switching from one HMM state to another.
Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.
A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM.
Hidden Markov model
A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states.
Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation.
Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation.
The general MF query format consists of a series of valid atomic symbols, with an optional number or range.
Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound.
An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification.
The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound.
SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation.
Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters.
Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters.
Non-sequence characters may be used for example for gaps.
Non-sequence characters may be used for gaps and translation stop.
Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters.
Alphabet for the consensus of two or more molecular sequences.
Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters.
Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters .
Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters.
Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters.
Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters.
Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters.
Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters.
Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters.
Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters.
A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
Format of an entry from the COG database of clusters of (related) protein sequences.
Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.
Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).
Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).
Report format for tandem repeats in a sequence (an EMBOSS report format).
Format of a report on exon-intron structure generated by EMBOSS est2genome.
Report format for restriction enzyme recognition sites used by EMBOSS restrict program.
Report format for restriction enzyme recognition sites used by EMBOSS restover program.
Report format for restriction enzyme recognition sites used by REBASE database.
This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)
Format of results of a sequence database search using FASTA.
This includes score data, alignment data and summary table.
Format of results of a sequence database search using some variant of BLAST.
Format of results of a sequence database search using some variant of MSPCrunch.
Format of results of a sequence database search using some variant of Smith Waterman.
Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.
The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
The hits are putative ligand-binding sequences and are found from a search of a sequence database.
Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.
Results format for searches of the InterPro database.
The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.
Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries.
The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.
Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.
Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.
Format of a regular expression pattern from the Prosite database.
A motif in the format generated by the MEME program.
Sequence profile (sequence classifier) format used in the PROSITE database.
A profile (sequence classifier) in the format used in the JASPAR database.
Format of the model of random sequences used by MEME.
Format of a hidden Markov model representation used by the HMMER package.
FASTA-style format for multiple sequences aligned by HMMER package to an HMM.
Format of multiple sequences aligned by DIALIGN package.
EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family.
The format is clustal-like and includes annotation of domain family classification information.
Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.
HMMER profile alignment (sequences versus HMMs)
Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.
HMMER profile alignment (HMM versus sequences)
Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.
Format of PHYLIP phylogenetic distance matrix data.
Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).
Dendrogram (tree file) format generated by ClustalW.
Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted.
Phylip continuous quantitative characters
PHYLIP file format for continuous quantitative character data.
PHYLIP file format for phylogenetics character frequency data.
Phylogenetic tree data format used by the PHYLIP program.
The format of an entry from the TreeBASE database of phylogenetic data.
The format of an entry from the TreeFam database of phylogenetic data.
Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.
Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).
The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.
Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).
Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server.
Vienna local RNA secondary structure format
Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server.
Format of an entry (or part of an entry) from the PDB database.
Entry format of PDB database in PDB format.
Entry format of PDB database in mmCIF format.
Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif
Entry format of PDB database in PDBML (XML) format.
Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.
Amino acid index format used by the AAindex database.
IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
Format of an entry from IntEnz (The Integrated Relational Enzyme Database).
Format of an entry from the BRENDA enzyme database.
Format of an entry from the KEGG REACTION database of biochemical reactions.
Format of an entry from the KEGG ENZYME database.
Format of an entry from the proto section of the REBASE enzyme database.
Format of an entry from the withrefm section of the REBASE enzyme database.
Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.
Format of output of the Pcons Model Quality Assessment Program (MQAP).
Format of output of the ProQ protein model quality predictor.
ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.
The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.
Entry format for the BIND database of protein interaction.
Entry format for the IntAct database of protein interaction.
This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.
Entry format for the textual abstract of signatures in an InterPro entry and its protein matches.
References are included and a functional inference is made where possible.
Entry format for the Gene3D protein secondary database.
Entry format for the PIRSF protein secondary database.
Entry format for the PRINTS protein secondary database.
Entry format for the Panther library of protein families and subfamilies.
Entry format for the Pfam protein secondary database.
Entry format for the SMART protein secondary database.
Entry format for the Superfamily protein secondary database.
Entry format for the TIGRFam protein secondary database.
Entry format for the ProDom protein domain classification database.
A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).
Entry format of Ensembl genome database.
Entry format of DictyBase genome database.
Entry format of Candida Genome database.
Entry format of DragonDB genome database.
Entry format of FlyBase genome database.
Entry format of Gramene genome database.
Entry format of KEGG GENES genome database.
Entry format of the Maize genetics and genomics database (MaizeGDB).
Entry format of the Mouse Genome Database (MGD).
Entry format of the Rat Genome Database (RGD).
Entry format of the Saccharomyces Genome Database (SGD).
Entry format of the Sanger GeneDB genome database.
Entry format of The Arabidopsis Information Resource (TAIR) genome database.
Entry format of the WormBase genomes database.
Entry format of the Zebrafish Information Network (ZFIN) genome database.
Entry format of the TIGR genome database.
Format of an entry from the OMIM database of genotypes and phenotypes.
Format of a record from the HGVbase database of genotypes and phenotypes.
Format of a record from the HIVDB database of genotypes and phenotypes.
Format of an entry from the KEGG DISEASE database.
Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program.
A format of raw sequence read data from an Applied Biosystems sequencing machine.
Format of MIRA sequence trace information file.
Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.
Sequence assembly project file EXP format.
Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata.
PHD sequence trace format to store serialised chromatogram data (reads).
Format of Affymetrix data file of raw image data.
Format of Affymetrix data file of information about (raw) expression levels of the individual probes.
Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.
Entry format for the ArrayExpress microarrays database.
Affymetrix experimental conditions data file format
Affymetrix data file format for information about experimental conditions and protocols.
Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.
Format of an entry from the Electron Microscopy DataBase (EMDB).
The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks.
The format of an entry from the MetaCyc metabolic pathways database.
The format of a report from the HumanCyc metabolic pathways database.
The format of an entry from the INOH signal transduction pathways database.
The format of an entry from the PATIKA biological pathways database.
The format of an entry from the reactome biological pathways database.
The format of an entry from the aMAZE biological pathways and molecular interactions database.
The format of an entry from the CPDB database.
The format of an entry from the Panther Pathways database.
Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
Format of mathematical models from the BioModel database.
The format of an entry from the KEGG LIGAND chemical database.
The format of an entry from the KEGG COMPOUND database.
The format of an entry from the KEGG PLANT database.
The format of an entry from the KEGG GLYCAN database.
The format of an entry from a database of chemical structures and property predictions.
ChEBI includes an ontological classification defining relations between entities or classes of entities.
The format of an entry from Chemical Entities of Biological Interest (ChEBI).
The format of an entry from the MSDchem ligand dictionary.
The format of an entry from the HET group dictionary (HET groups from PDB files).
The format of an entry from the KEGG DRUG database.
Format of bibliographic reference as used by the PubMed database.
Bibliographic reference information including citation information is included
Format for abstracts of scientific articles from the Medline database.
CiteXplore 'core' citation format including title, journal, authors and abstract.
CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references.
Article format of the PubMed Central database.
Text mining abstract format from the Oscar 3 application.
Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document.
Format of an ATOM record (describing data for an individual atom) from a PDB file.
Format of CATH domain classification information for a polypeptide chain.
The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.
The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.
Format of CATH domain classification information for a protein PDB file.
Entry (gene) format of the NCBI database.
This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.
Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service.
Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database.
Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB).
Map of a plasmid (circular DNA) in PlasMapper TextMap format.
Phylogenetic tree TreeCon (text) format.
The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format.
File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages.
Closely related concept focusing on the specification of a data format.
GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials.
Format can be a quality of a data record.
A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.)
Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format.
Data format for a molecular sequence record.
Data format for molecular sequence feature information.
Data format for molecular sequence alignment information.
Fasta format variant with database name before ID.
FASTQ short read format ignoring quality scores.
FASTQ short read format with phred quality.
FASTQ Solexa/Illumina 1.0 short read format.
GFF feature file format with sequence in the header.
FASTA sequence format including NCBI-style GIs.
Intelligenetics sequence format (strict version).
Jackknifer interleaved and non-interleaved sequence format.
Mega interleaved and non-interleaved sequence format.
GCG MSF (multiple sequence file) file format.
PDB nucleotide sequence format (ATOM lines).
PDB nucleotide sequence format (SEQRES lines).
Plain old FASTA sequence format (unspecified format for IDs).
Raw sequence format with no non-sequence characters.
Stockholm multiple sequence alignment format (used by Pfam and Rfam).
Plain text sequence format (essentially unformatted).
DAS sequence (XML) format (nucleotide-only).
EMBOSS debugging trace sequence format of full internal data content.
Jackknifer output sequence non-interleaved format.
Mega non-interleaved output sequence format.
NCBI FASTA sequence format with NCBI-style IDs.
Nexus/paup non-interleaved sequence format.
General Feature Format (GFF) of sequence features.
Generic Feature Format version 3 (GFF3) of sequence features.
EMBOSS debugging trace feature format of full internal data content.
ClustalW format for (aligned) sequences.
EMBOSS alignment format for debugging trace of full internal data content.
Alignment format for start and end of matches between sequence pairs.
Mega format for (typically aligned) sequences.
Mega non-interleaved format for (typically aligned) sequences.
Nexus/paup format for (aligned) sequences.
Nexus/paup non-interleaved format for (aligned) sequences.
EMBOSS simple sequence pair alignment format.
Phylip non-interleaved format for (aligned) sequences.
Alignment format for score values for pairs of sequences.
EMBOSS simple multiple alignment format.
Simple multiple sequence (alignment) format for SRS.
Simple sequence pair (alignment) format for SRS.
Data format for a biological pathway or network.
Data format for a sequence-profile alignment.
Data format for a sequence-HMM profile alignment.
Data format for a full-text scientific article.
Data format for an abstract (report) from text mining.
Data format for reports on enzyme kinetics.
Format of a report on a chemical compound.
Format of a report on a particular locus, gene, gene system or groups of genes.
Data format for a molecular tertiary structure.
Format of raw (unplotted) phylogenetic data.
Phylogenetic continuous quantitative character format
Format of phylogenetic continuous quantitative character data.
Format of phylogenetic discrete states data.
Phylogenetic tree report (cliques) format
Phylogenetic tree report (invariants) format
Annotation format for electron microscopy models.
Phylogenetic tree report (tree distances) format
Format for phylogenetic tree distance data.
Format for microarray experimental data.
Format for sequence trace data (i.e. including base call information).
Genotype and phenotype annotation format
Format of a report on genotype / phenotype information.
Format of a map of (typically one) molecular sequence annotated with features.
Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence.
Format of a report of general information about a specific protein.
Format of a report of general information about a specific enzyme.
Format of a matrix of 3D-1D scores (amino acid environment probabilities).
Protein structure report (quality evaluation) format
Format of a report on the quality of a protein three-dimensional model.
Format of a report on sequence hits and associated data from searching a sequence database.
Format of a matrix of genetic distances between molecular sequences.
Data format of a dirichlet distribution.
HMM emission and transition counts format
Data format for the emission and transition counts of a hidden Markov model.
Format for secondary structure (predicted or real) of an RNA molecule.
Format for secondary structure (predicted or real) of a protein molecule.
Format used to specify range(s) of sequence positions.
Alphabet for molecular sequence with possible unknown positions but without non-sequence characters.
Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters.
Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters.
Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters.
Format used for map of repeats in molecular (typically nucleotide) sequences.
Nucleic acid features (restriction sites) format
Format used for report on restriction enzyme recognition sites in nucleotide sequences.
Format used for report on coding regions in nucleotide sequences.
Format used for clusters of molecular sequences.
Format used for clusters of protein sequences.
Format used for clusters of nucleotide sequences.
A text format resembling EMBL entry format.
This concept may be used for the many non-standard EMBL-like text formats.
This concept may be used for non-standard FASTQ short read-like formats.
A text format resembling FASTQ short read format.
A text sequence format resembling uniprotkb entry format.
Abstract format used by MedLine database.
A serialisation format conforming to the Open Biomedical Ontologies (OBO) model.
A serialisation format conforming to the Web Ontology Language (OWL) model.
This concept may also be used for the many non-standard FASTA-like formats.
Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database.
Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment.
This is a placeholder for other more specific concepts. It should not normally be used for annotation.
This concept may be used for the non-standard GenBank-like text formats.
A text format resembling GenBank entry (plain text) format.
Text format for a sequence feature table.
Format of a report on organism strain data / cell line.
Format for a report of strain data as used for CIP database entries.
PHYLIP file format for phylogenetic property data.
Entry format (HTML) for the STRING database of protein interaction.
Entry format (XML) for the STRING database of protein interaction.
GFF feature format (of indeterminate version).
Gene Transfer Format (GTF), a restricted version of GFF.
EMBL entry format wrapped in HTML elements.
Format of an entry from the BioCyc enzyme database.
Format of an entry from the Enzyme nomenclature database (ENZYME).
Format of a report on a gene from the PseudoCAP database.
Format of a report on a gene from the GeneCards database.
Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).
fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats.
Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format.
eXtensible Markup Language (XML) format.
Data in XML format can be serialised into text, or binary format.
Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.
Typical textual representation of a URI.
The format of an entry from the NCI-Nature pathways database.
A broad class of format distinguished by the scientific nature of the data that is identified.
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.
BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more).
A serialisation format conforming to the Resource Description Framework (RDF) model.
Genbank entry format wrapped in HTML elements.
Format of a report on protein features (domain composition).
This concept may be used for the many non-standard EMBL-like formats.
A format resembling EMBL entry (plain text) format.
A format resembling FASTQ short read format.
This concept may be used for the many non-standard FASTA-like formats.
A sequence format resembling uniprotkb entry format.
XML format for a sequence feature table.
Text format for molecular sequence alignment information.
XML format for molecular sequence alignment information.
This concept may be used for the any non-standard EMBL-like XML formats.
An XML format resembling EMBL entry format.
This concept may be used for the non-standard GenBank-like formats.
A format resembling GenBank entry (plain text) format.
Entry format for the STRING database of protein interaction.
Text format (representation) of amino acid residues.
Alphabet for a molecular sequence without any unknown positions or ambiguity characters.
Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters.
Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters .
Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters.
completely unambiguous pure rna sequence
Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters.
Format of a raw molecular sequence (i.e. the alphabet used).
BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.
Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation.
Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters.
Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences.
Format of sequence variation annotation.
Some variant of Pearson MARKX alignment format.
Some variant of Mega format for (typically aligned) sequences.
Some variant of Phylip format for (aligned) sequences.
AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).
AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.
ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).
Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser.
BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).
bigBed format for large sequence annotation tracks, similar to textual BED format.
Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.
bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format.
PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.
Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.
Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.
2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'.
.nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'.
genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.
genePred table format for gene prediction tracks.
Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.
axt format of alignments, typically produced from BLASTZ.
LAV format of alignments generated by BLASTZ and LASTZ.
Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).
Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive.
ZTR format for storing chromatogram data from DNA sequencing instruments.
Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation.
BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
Format of a matrix (array) of numerical values.
Format of data concerning the classification of the sequences and/or structures of protein structural domain(s).
Format of raw SCOP domain classification data files.
Format of raw CATH domain classification data files.
Format of summary of domain classification information for a CATH domain.
Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models.
BioPAX is an exchange format for pathway data, with its data model defined in OWL.
EBI Application Result XML is a format returned by sequence similarity search Web services at EBI.
XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI.
phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data.
NeXML is a standardised XML format for rich phyloinformatic data.
MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED).
MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED).
GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC).
GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG).
Biological pathway or network report format
Data format for a report of information derived from a biological pathway or network.
Data format for annotation on a laboratory experiment.
Cytoband format for chromosome cytobands.
CellML, the format for mathematical models of biological and other networks.
Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI.
Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema.
mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.
mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.
TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS.
mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines.
mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics.
GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS.
spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics.
A human-readable encoding for the Web Ontology Language (OWL).
This format was influenced by the OWL Abstract Syntax and the DL style syntax.
A syntax for writing OWL class expressions.
A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort".
The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs.
The SPARQL Query Language incorporates a very similar syntax.
A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format.
N-Triples should not be confused with Notation 3 which is a superset of Turtle.
A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind.
RDF/XML is a serialization syntax for OWL DL, but not for OWL Full.
Resource Description Framework (RDF) XML format.
The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA.
Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.
The MAP file describes SNPs and is used by the Plink package.
The PED file describes individuals and genetic data and is used by the Plink package.
Data format for a metadata on an individual and their genetic data.
The PED/MAP file describes data used by the Plink package.
File format of a CT (Connectivity Table) file from the RNAstructure package.
Format for the Genetic Data Environment (GDE).
A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge.
HMMER profile HMM file for HMMER versions 2.x
HMMER profile HMM file for HMMER versions 3.x
XML format as produced by the NCBI Blast package
A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
Operation is a function that is computational. It typically has input(s) and output(s), which are always data.
Process can have a function (as its quality/property), and can also have (perform) an operation with inputs and outputs.
However, operation is not a GFO 'Concept' present only in someone's mind.
Operation is a function that is computational. It typically has input(s) and output(s), which are always data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'.
Method may in addition focus on how to achieve the result, not just on what to achieve as with operation.
However, one may think that an operation is not a process and not a physical entity.
Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs.
BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s).
Computational tool provides one or more operations.
However, one may think that an operation is not a process.
Function, including an operation, can be a quality/property of e.g. a computational tool.
GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials.
Function, including an operation, can have a role of a quality/property in semantic annotation of e.g. a computational tool.
Search or query a data resource and retrieve entries and / or annotation.
Data retrieval (database cross-reference)
Search database to retrieve all relevant references to a particular entity or entry.
This is a broad concept and is used a placeholder for other, more specific concepts.
Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.
Generate an index of (typically a file of) biological data.
Retrieve basic information about a molecular sequence.
Generate a molecular sequence by some means.
Edit or change a molecular sequence, either randomly or specifically.
Merge two or more (typically overlapping) molecular sequences.
Convert a molecular sequence from one type to another.
Calculate sequence complexity, for example to find low-complexity regions in sequences.
Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes.
Calculate character or word composition or frequency of a molecular sequence.
Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
Find and/or analyse repeat sequences in (typically nucleotide) sequences.
Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery).
Motifs and patterns might be conserved or over-represented (occur with improbable frequency).
Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s).
Find motifs shared by molecular sequences.
Transcription regulatory sequence analysis
Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences.
For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
Conserved transcription regulatory sequence identification
Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites).
For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
Protein property calculation (from structure)
This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure.
Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.
Analyse flexibility and motion in protein structure.
Protein structural feature identification
This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
Identify or screen for 3D structural motifs in protein structure(s).
Identify structural domains in a protein structure from first principles (for example calculations on structural compactness).
Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s).
Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).
Calculate, visualise or analyse phi/psi angles of a protein structure.
This includes methods to render and visualise the properties of a protein sequence.
Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence.
Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.
This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.
Extract a sequence feature table from a sequence database entry.
Query the features (in a feature table) of molecular sequence(s).
Compare the feature tables of two or more molecular sequences.
Display basic information about a sequence alignment.
Compare (typically by aligning) two molecular sequence alignments.
Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence).
Process (read and / or write) physicochemical property data of nucleic acids.
Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence.
Predict splicing alternatives or transcript isoforms from analysis of sequence data.
Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
Detect frameshift errors in DNA sequences (from sequencing projects).
Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences.
Predict secondary structure of protein sequences.
Secondary structure prediction (protein)
Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.
Protein super-secondary structure prediction
Predict super-secondary structure of protein sequence(s).
Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences.
Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.
Predict tertiary structure of a molecular (biopolymer) sequence.
Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences.
Methods usually involve multiple sequence alignment analysis.
Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
Protein-protein interaction prediction (from protein sequence)
Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences.
Protein-protein interaction prediction (from protein structure)
Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures.
Analyse a network of protein interactions.
Compare two or more networks of protein interactions.
Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).
Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data.
Data retrieval (restriction enzyme annotation)
Retrieve information on restriction enzymes or restriction enzyme sites.
Restriction enzyme information retrieval
A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
Identify genetic markers in DNA sequences.
Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.
Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.
This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.
Calculate codon usage statistics and create a codon usage table.
Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences.
Identify and plot third base position variability in a nucleotide sequence.
Find exact character or word matches between molecular sequences without full sequence alignment.
Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences.
Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria.
Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
The clusters may be output or used internally for some other purpose.
Align (identify equivalent sites within) molecular sequences.
Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA).
Structure-based sequence alignment construction
Align molecular sequences using sequence and structural information.
Align (superimpose) molecular tertiary structures.
Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment.
Generate some type of structural (3D) profile or template from a structure or structure alignment.
Align sequence profiles (representing sequence alignments).
See also 'Sequence alignment comparison'.
Structural (3D) profile alignment construction
Align structural (3D) profiles or templates (representing structures or structure alignments).
A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Align molecular sequence(s) to sequence profile(s).
Sequence-3D profile alignment construction
Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment).
Align molecular sequence to structure in 3D space (threading).
Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
Recognize (predict and identify) known protein structural domains or folds in protein sequence(s).
Data retrieval (metadata and documentation)
This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.
Query the biomedical and informatics literature.
Process and analyse text (typically the biomedical and informatics literature) to extract information from it.
Design or predict oligonucleotide primers for PCR and DNA amplification etc.
Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families.
Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
Microarray data standardization and normalization
This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc.
Standardize or normalize microarray data.
Sequencing-based expression profile data processing
Process (read and / or write) SAGE, MPSS or SBS experimental data.
Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles.
Generate a gene expression profile or pattern, for example from microarray data.
Compare gene expression profiles or patterns.
Interpret (in functional terms) and annotate gene expression data.
For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
Methods will typically navigate a graph of protein families of known structure.
Identify and select targets for protein structural determination.
Assign secondary structure from protein coordinate or experimental data.
Assign a protein tertiary structure (3D coordinates) from raw experimental data.
Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc.
Evaluate the quality or correctness a protein three-dimensional model.
The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
Refine (after evlauation) a model of protein structure to reduce steric clashes, volume irregularities etc.
Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.
Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.
For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.
Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).
A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.
Predict the folding pathway(s) or non-native structural intermediates of a protein.
Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s).
Methods might predict silent or pathological mutations.
Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.
Design molecules that elicit an immune response (immunogens).
Zinc finger protein domain prediction and optimisation
Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
Calculate Km, Vmax and derived data for an enzyme reaction.
Reformat a file of data (or equivalent entity in memory).
Test and validate the format and content of a data file.
Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.
This excludes direct retrieval methods (e.g. the dbfetch program).
Search a sequence database by sequence comparison and retrieve similar sequences.
Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data.
Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group.
Methods might use fingerprints, profiles, hidden Markov models, sequence alignment etc to provide a mapping to a secondary database (Prosite, Blocks, ProDom, Prints, Pfam etc.).
Screen a sequence against a motif or pattern database.
Search a database of sequence profiles with a query sequence.
Search a database of transmembrane proteins, for example for sequence or structural similarities.
Query a database and retrieve sequences with a given entry code or accession number.
Query a database and retrieve sequences containing a given keyword.
Search a sequence database and retrieve sequences that are similar to a query sequence.
Sequence database search (by motif or pattern)
Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression.
Sequence database search (by amino acid composition)
Search a sequence database and retrieve sequences of a given amino acid composition.
Sequence database search (by physicochemical property)
Search a sequence database and retrieve sequences with a specified physicochemical property.
Sequence database search (by sequence using word-based methods)
Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method.
Sequence similarity search (word-based methods)
Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.
Sequence database search (by sequence using profile-based methods)
Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query.
Sequence similarity search (profile-based methods)
Sequence database search (by sequence using local alignment-based methods)
This includes tools based on the Smith-Waterman algorithm or FASTA.
Sequence similarity search (local alignment-based methods)
Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method.
Sequence database search (by sequence using global alignment-based methods)
Sequence similarity search (global alignment-based methods)
Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method.
This includes tools based on the Needleman and Wunsch algorithm.
Sequence database search (by sequence for primer sequences)
Sequence similarity search (primer sequences)
STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences.
Sequence database search (by molecular weight)
Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry.
Sequence database search (by isoelectric point)
Search sequence(s) or a sequence database for sequences of a given isoelectric point.
Query a tertiary structure database and retrieve entries with a given entry code or accession number.
Query a tertiary structure database and retrieve entries containing a given keyword.
Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence.
Structure database search (by structure)
Search a tertiary structure database and retrieve structures that are similar to a query structure.
Annotate a molecular sequence record with terms from a controlled vocabulary.
Annotate a genome sequence with terms from a controlled vocabulary.
Nucleic acid sequence reverse and complement
Generate the reverse and / or complement of a nucleotide sequence.
Generate a random sequence, for example, with a specific character composition.
Generate digest fragments for a nucleotide sequence containing restriction sites.
Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses.
Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition.
For example, SNPs or repeats in a DNA sequence might be masked.
Mask characters in a molecular sequence (replacing those characters with a mask character).
Cut (remove) characters or a region from a molecular sequence.
Create (or remove) restriction sites in sequences, for example using silent mutations.
Transcribe a nucleotide sequence into mRNA sequence(s).
Sequence composition calculation (nucleic acid)
Calculate base frequency or word composition of a nucleotide sequence.
Sequence composition calculation (protein)
Calculate amino acid frequency or word composition of a protein sequence.
Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences.
Analyse repeat sequence organization such as periodicity.
Protein hydropathy calculation (from structure)
Analyse the hydrophobic, hydrophilic or charge properties of a protein structure.
Protein solvent accessibility calculation
Calculate solvent accessible or buried surface areas in protein structures.
Identify clusters of hydrophobic or charged residues in a protein structure.
Calculate whether a protein structure has an unusually large net charge (dipole moment).
Protein surface and interior calculation
Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc.
Binding site prediction (from structure)
Ligand-binding and active site prediction (from structure)
Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures.
Protein-nucleic acid binding site analysis
Analyse RNA or DNA-binding sites in protein structure.
Decompose a structure into compact or globular fragments (protein peeling).
Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure.
Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure.
Calculate clusters of contacting residues in protein structures.
Cluster of contacting residues might be key structural residues.
Identify potential hydrogen bonds between amino acids and other groups.
The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.
Residue non-canonical interaction detection
Calculate non-canonical atomic interactions in protein structures.
Calculate a Ramachandran plot of a protein structure.
Analyse (typically to validate) a Ramachandran plot of a protein structure.
Calculate the molecular weight of a protein sequence or fragments.
Protein extinction coefficient calculation
Predict extinction coefficients or optical density of a protein sequence.
Protein pH-dependent property calculation
Calculate pH-dependent properties from pKa calculations of a protein sequence.
Protein hydropathy calculation (from sequence)
Hydropathy calculation on a protein sequence.
Calculate isoelectric point of a protein sequence.
Protein hydrogen exchange rate calculation
Estimate hydrogen exchange rate of a protein sequence.
Calculate hydrophobic or hydrophilic / charged regions of a protein sequence.
Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein.
Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity.
Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc.
Predict the solubility or atomic solvation energy of a protein sequence.
Predict crystallizability of a protein sequence.
Protein signal peptide detection (eukaryotes)
Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins.
Protein signal peptide detection (bacteria)
Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins.
Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc.
Protein feature prediction (from sequence)
Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure.
Methods typically involve scanning for known motifs, patterns and regular expressions.
Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.
Sequence feature detection (nucleic acid)
Predict antigenic determinant sites (epitopes) in protein sequences.
Protein post-translation modification site prediction
Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.
Predict post-translation modification sites in protein sequences.
Detect or predict signal peptides and signal peptide cleavage sites in protein sequences.
Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
Ligand-binding and active site prediction (from sequence)
Predict catalytic residues, active sites or other ligand-binding sites in protein sequences.
Predict RNA and DNA-binding binding sites in protein sequences.
Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization.
Detect or predict cleavage sites (enzymatic or chemical) in protein sequences.
Predict epitopes that bind to MHC class I molecules.
Predict epitopes that bind to MHC class II molecules.
Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc.
Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.
Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
Detect or predict transposons, retrotransposons / retrotransposition signatures etc.
Detect polyA signals in nucleotide sequences.
Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
Detect quadruplex-forming motifs in nucleotide sequences.
Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.
An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.
Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map.
Nucleosome formation or exclusion sequence prediction
Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.
Methods might require a pre-mRNA or genomic DNA sequence.
Identify, predict or analyse splice sites in nucleotide sequences.
Predict whole gene structure using a combination of multiple methods to achieve better predictions.
Find operons (operators, promoters and genes) in bacteria genes.
Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences.
Selenocysteine insertion sequence (SECIS) prediction
SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.
Predict selenocysteine insertion sequence (SECIS) in a DNA sequence.
Transcription regulatory element prediction
This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences.
Predict translation initiation sites, possibly by searching a database of sites.
Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.
Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences.
Transcription regulatory element prediction (DNA-cis)
Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences.
Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.
Transcription regulatory element prediction (RNA-cis)
Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences.
Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
Transcription regulatory element prediction (trans)
Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets.
Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
Matrix/scaffold attachment site prediction
Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences.
MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
Transcription factor binding site prediction
Identify or predict transcription factor binding sites in DNA sequences.
Identify or predict exonic splicing enhancers (ESE) in exons.
An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.
Evaluate molecular sequence alignment accuracy.
Evaluation might be purely sequence-based or use structural information.
Sequence alignment analysis (conservation)
Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.
Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.
Sequence alignment analysis (site correlation)
This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
Analyse correlations between sites in a molecular sequence alignment.
Sequence alignment analysis (chimeric sequence detection)
Detects chimeric sequences (chimeras) from a sequence alignment.
A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.
Sequence alignment analysis (recombination detection)
Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment.
Sequence alignment analysis (indel detection)
Identify insertion, deletion and duplication events from a sequence alignment.
Nucleosome formation potential prediction
Predict nucleosome formation potential of DNA sequences.
Nucleic acid thermodynamic property calculation
Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy.
A melting profile is used to visualise and analyse partly melted DNA conformations.
Calculate and plot a DNA or DNA/RNA melting profile.
Calculate and plot a DNA or DNA/RNA stitch profile.
A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.
Calculate and plot a DNA or DNA/RNA melting curve.
Nucleic acid probability profile plotting
Calculate and plot a DNA or DNA/RNA probability profile.
Nucleic acid temperature profile plotting
Calculate and plot a DNA or DNA/RNA temperature profile.
Calculate curvature and flexibility / stiffness of a nucleotide sequence.
Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence.
Identify or predict tRNA genes in genomic sequences (tRNA).
Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences.
Protein secondary structure prediction (integrated)
Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions.
Protein secondary structure prediction (helices)
Predict helical secondary structure of protein sequences.
Protein secondary structure prediction (turns)
Predict turn structure (for example beta hairpin turns) of protein sequences.
Protein secondary structure prediction (coils)
Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences.
Protein secondary structure prediction (disulfide bonds)
Predict cysteine bonding state and disulfide bond partners in protein sequences.
Predict G protein-coupled receptors (GPCR).
G protein-coupled receptor (GPCR) prediction
G protein-coupled receptor (GPCR) analysis
Analyse G-protein coupled receptor proteins (GPCRs).
Predict tertiary structure (backbone and side-chain conformation) of protein sequences.
Methods might identify thermodynamically stable or evolutionarily conserved structures.
Predict tertiary structure of DNA or RNA.
Predict tertiary structure of protein sequence(s) without homologs of known structure.
The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.
Build a three-dimensional protein model based on known (for example homologs) structures.
This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.
Model the structure of a protein in complex with a small molecule or another macromolecule.
Methods might require a preliminary C(alpha) trace.
Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.
Methods might use a residue rotamer library.
Model loop conformation in protein structures.
Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme.
Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques.
Structured RNA prediction and optimisation
Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection.
Nucleic acid folding family identification
This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
Single nucleotide polymorphism detection
Find single nucleotide polymorphisms (SNPs) between sequences.
Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers.
Map the genetic architecture of dynamic complex traits.
This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.
Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.
Predict genetic code from analysis of codon usage data.
Draw a dotplot of sequence similarities identified from word-matching or character comparison.
Pairwise sequence alignment construction
Multiple sequence alignment construction
This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.
Pairwise sequence alignment construction (local)
Local alignment methods identify regions of local similarity.
Local pairwise sequence alignment construction
Locally align exactly two molecular sequences.
Pairwise sequence alignment construction (global)
Global alignment methods identify similarity across the entire length of the sequences.
Globally align exactly two molecular sequences.
Global pairwise sequence alignment construction
Multiple sequence alignment construction (local)
Locally align two or more molecular sequences.
Local multiple sequence alignment construction
Multiple sequence alignment construction (global)
Global multiple sequence alignment construction
Globally align two or more molecular sequences.
Multiple sequence alignment construction (constrained)
Constrained multiple sequence alignment construction
Multiple sequence alignment (constrained)
Align two or more molecular sequences with user-defined constraints.
Multiple sequence alignment construction (consensus)
Align two or more molecular sequences using multiple methods to achieve higher quality.
Consensus multiple sequence alignment construction
Multiple sequence alignment construction (phylogenetic tree-based)
Multiple sequence alignment (phylogenetic tree-based)
Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.
Phylogenetic tree-based multiple sequence alignment construction
This is supposed to give a more biologically meaningful alignment than standard alignments.
Secondary structure alignment construction
Align molecular secondary structure (represented as a 1D string).
Protein secondary structure alignment construction
RNA secondary structure alignment construction
Pairwise structure alignment construction
Align (superimpose) exactly two molecular tertiary structures.
Multiple structure alignment construction
This includes methods that use an existing alignment.
Align (superimpose) two or more molecular tertiary structures.
Pairwise structure alignment construction (local)
Local alignment methods identify regions of local similarity, common substructures etc.
Locally align (superimpose) exactly two molecular tertiary structures.
Local pairwise structure alignment construction
Pairwise structure alignment construction (global)
Globally align (superimpose) exactly two molecular tertiary structures.
Global alignment methods identify similarity across the entire structures.
Global pairwise structure alignment construction
Multiple structure alignment construction (local)
Locally align (superimpose) two or more molecular tertiary structures.
Local multiple structure alignment construction
Multiple structure alignment construction (global)
Globally align (superimpose) two or more molecular tertiary structures.
Global multiple structure alignment construction
Sequence profile alignment construction (pairwise)
Pairwise sequence profile alignment construction
Sequence profile alignment construction (multiple)
Multiple sequence profile alignment construction
Structural (3D) profile alignment construction (pairwise)
Align exactly two molecular Structural (3D) profiles.
Structural (3D) profile alignment (pairwise)
Pairwise structural (3D) profile alignment construction
Structural (3D) profile alignment construction (multiple)
Structural (3D) profile alignment (multiple)
Multiple structural (3D) profile alignment construction
Align two or more molecular 3D profiles.
Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function.
Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword.
PCR primer design (for large scale sequencing)
Predict primers for large scale sequencing.
PCR primer design (for genotyping polymorphisms)
Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs).
PCR primer design (for gene transcription profiling)
Predict primers for gene transcription profiling.
PCR primer design (for conserved primers)
Predict primers that are conserved across multiple genomes or species.
PCR primer design (based on gene structure)
Predict primers based on gene structure, promoters, exon-exon junctions etc.
PCR primer design (for methylation PCRs)
The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.
Sequence assembly by combining fragments using an existing backbone sequence.
De-novo assemblers are much slower and more memory intensive than mapping assemblers.
Sequence assembly by combining fragments into a new, previously unknown sequence.
Sequence assembly capable on a very large scale such as assembly of whole genomes.
Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.
Sequence assembly for EST sequences (transcribed mRNA).
Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome.
Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts.
Process (read and / or write) serial analysis of gene expression (SAGE) data.
Serial analysis of gene expression data processing
Massively parallel signature sequencing data processing
Process (read and / or write) massively parallel signature sequencing (MPSS) data.
Process (read and / or write) sequencing by synthesis (SBS) data.
Generate a heat map of gene expression from microarray data.
The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions.
Analyse one or more gene expression profiles, typically to interpret them in functional terms.
Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway.
Protein secondary structure assignment (from coordinate data)
Assign secondary structure from protein coordinate data.
Protein secondary structure assignment (from CD data)
Assign secondary structure from circular dichroism (CD) spectroscopic data.
Protein structure assignment (from X-ray crystallographic data)
Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data.
Protein structure assignment (from NMR data)
Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data.
Phylogenetic tree construction (data centric)
Construct a phylogenetic tree from a specific type of data.
Phylogenetic tree construction (method centric)
Construct a phylogenetic tree using a specific method.
Phylogenetic tree construction (from molecular sequences)
Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.
Phylogenetic tree construction from molecular sequences.
Phylogenetic tree construction (from continuous quantitative characters)
Phylogenetic tree construction from continuous quantitative character data.
Phylogenetic tree construction (from gene frequencies)
Phylogenetic tree construction from gene frequency data.
Phylogenetic tree construction (from polymorphism data)
Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data.
Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison.
Phylogenetic tree construction (parsimony methods)
This includes evolutionary parsimony (invariants) methods.
Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment.
Phylogenetic tree construction (minimum distance methods)
Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances.
This includes neighbor joining (NJ) clustering method.
Phylogenetic tree construction (maximum likelihood and Bayesian methods)
Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.
Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.
Phylogenetic tree construction (quartet methods)
Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely.
Phylogenetic tree construction (AI methods)
Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms.
Sequence alignment analysis (phylogenetic modelling)
Identify a plausible model of DNA substitution that explains a DNA sequence alignment.
Analyse the shape (topology) of a phylogenetic tree.
Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree.
Phylogenetic tree analysis (gene family prediction)
Predict families of genes and gene function based on their position in a phylogenetic tree.
Phylogenetic tree analysis (natural selection)
Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).
Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.
Phylogenetic tree construction (consensus)
Methods typically test for topological similarity between trees using for example a congruence index.
Compare two or more phylogenetic trees to produce a consensus tree.
Compare two or more phylogenetic trees to detect subtrees or supertrees.
Compare two or more phylogenetic trees to calculate distances between trees.
Annotate a phylogenetic tree with terms from a controlled vocabulary.
Peptide immunogen prediction and optimisation
Predict and optimise peptide ligands that elicit an immunological response.
Predict or optimise DNA to elicit (via DNA vaccination) an immunological response.
Reformat (a file or other report of) molecular sequence(s).
Reformat (a file or other report of) molecular sequence alignment(s).
Visualise, format or render a molecular sequence, possibly with sequence features or properties shown.
Visualise, format or print a molecular sequence alignment.
Visualise, format or render sequence clusters.
Visualise RNA secondary structure, knots, pseudoknots etc.
Render and visualise protein secondary structure.
Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation.
Identify and analyse networks of protein interactions.
Visualise restriction maps in DNA sequences.
Draw a circular maps of DNA, for example a plasmid map.
Identify folding families of related RNAs.
Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.
Retrieve existing annotation (or documentation), typically annotation on a database entity.
Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
Predict general functional properties of a protein.
Compare the functional properties of two or more proteins.
Submit a molecular sequence to a database.
Analyse a known network of gene regulation.
Prepare or load a user-specified data file so that it is available for use.
This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
Query a sequence data resource (typically a database) and retrieve sequences and / or annotation.
Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation.
This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
A dot has three coordinates (x,y,z) and (typically) a color.
Calculate the positions of dots that are homogeneously distributed over the surface of a molecule.
Protein atom surface calculation (accessible)
Calculate the solvent accessibility ('accessible surface') for each atom in a structure.
Protein atom surface calculation (accessible molecular)
Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure.
Protein residue surface calculation (accessible)
Calculate the solvent accessibility ('accessible surface') for each residue in a structure.
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
Protein residue surface calculation (vacuum accessible)
Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
Protein residue surface calculation (accessible molecular)
Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure.
Protein residue surface calculation (vacuum molecular)
Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
Protein surface calculation (accessible molecular)
Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole.
Protein surface calculation (accessible)
Calculate the solvent accessibility ('accessible surface') for a structure as a whole.
Calculate for each residue in a protein structure all its backbone torsion angles.
Calculate for each residue in a protein structure all its torsion angles.
Calculate for each cysteine (bridge) all its torsion angles.
For each amino acid in a protein structure calculate the backbone angle tau.
Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
Detect cysteine bridges (from coordinate data) in a protein structure.
Detect free cysteines in a protein structure.
A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.
Detect cysteines that are bound to metal in a protein structure.
Residue contact calculation (residue-nucleic acid)
Calculate protein residue contacts with nucleic acids in a structure.
Residue contact calculation (residue-metal)
Calculate protein residue contacts with metal in a structure.
Residue contact calculation (residue-negative ion)
Calculate ion contacts in a structure (all ions for all side chain atoms).
Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance.
A symmetry contact is a contact between two atoms in different asymmetric unit.
Calculate the number of symmetry contacts made by residues in a protein structure.
Residue contact calculation (residue-ligand)
Calculate contacts between residues and ligands in a protein structure.
Calculate (and possibly score) salt bridges in a protein structure.
Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.
Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein.
Identify poorly packed residues in protein structures.
Identify for each residue in a protein structure any improper dihedral (phi/psi) angles.
Extract a molecular sequence from a PDB file.
A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
Determine for residue the DSSP determined secondary structure in three-state (HSC).
Reformat (a file or other report of) tertiary structure data.
Protein cysteine and disulfide bond assignment
Assign cysteine bonding state and disulfide bond partners in protein structures.
The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).
Identify poor quality amino acid positions in protein structures.
Query a tertiary structure database and retrieve water molecules.
Identify or predict siRNA duplexes in RNA.
Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses).
Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, or create a file of sequences.
Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences.
Process (read and / or write) physicochemical property data for small molecules.
Search and retrieve documentation on a bioinformatics ontology.
Query an ontology and retrieve concepts or relations.
Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences.
Perform basic (non-analytical) operations on a file of molecular tertiary structural data.
This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
Query a profile data resource and retrieve one or more profile(s) and / or associated annotation.
Perform a statistical data operation of some type, e.g. calibration or validation.
Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data.
A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.
Visualise transmembrane proteins, typically the transmembrane regions within a sequence.
An operation performing purely illustrative (pedagogical) purposes.
Query a biological pathways database and retrieve annotation on one or more pathways.
Query a database and retrieve one or more data identifiers.
Calculate a density plot (of base composition) for a nucleotide sequence.
Analyse one or more known molecular sequences.
Process (read and / or write) molecular sequence motifs.
Process (read and / or write) protein interaction data.
Analyse protein tertiary structural data.
Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity.
Analyse features in molecular sequences.
Process (read and / or write) a data file (or equivalent entity in memory). Processing is limited to basic (non-analytical) operations.
Analyse gene expression and regulation data.
Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type.
Process (read and / or write) an index of (typically a file of) biological data.
Process (read and / or write) some type of sequence profile.
Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report.
Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report.
Analyse known protein secondary structure data.
Physicochemical property data processing
Process (read and / or write) data on the physicochemical property of a molecule.
Predict oligonucleotide primers or probes.
Process (read and / or write) data of a specific type, for example applying analytical methods.
Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.
Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.
Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords.
Predict, recognise, detect or identify some properties of a biomolecule.
Compare two or more things to identify similarities.
Model or simulate some biological entity or system.
Perform basic operations on some data or a database.
Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.
Design a biological entity (typically a molecular sequence or structure) with specific properties.
Process (read and / or write) microarray data.
Process (read and / or write) a codon usage table.
Retrieve a codon usage table and / or associated annotation.
Process (read and / or write) a gene expression profile.
Annotate a gene expression profile with concepts from an ontology of gene functions.
Generate, analyse or handle a biological pathway or network.
Process (read and / or write) RNA secondary structure data.
Process (read and / or write) RNA tertiary structure data.
Process (read and / or write) a phylogenetic tree.
Process (read and / or write) protein secondary structure data.
Process (read and / or write) a network of protein interactions.
Process (read and / or write) one or more molecular sequences and associated annotation.
Process (read and / or write) a protein sequence and associated annotation.
Process (read and / or write) a nucleotide sequence and associated annotation.
Compare two or more molecular sequences.
Process (read and / or write) a sequence cluster.
Process (read and / or write) a sequence feature table.
Detect, predict and identify genes or components of genes in DNA sequences.
Classify G-protein coupled receptors (GPCRs) into families and subfamilies.
G protein-coupled receptor (GPCR) classification
Predict G-protein coupled receptor (GPCR) coupling selectivity.
Process (read and / or write) a protein tertiary structure.
Calculate the solvent accessibility for each atom in a structure.
Calculate the solvent accessibility for each residue in a structure.
Calculate the solvent accessibility of a structure as a whole.
Process (read and / or write) a molecular sequence alignment.
Identify or predict protein-protein interactions, interfaces, binding sites etc.
Process (read and / or write) a molecular tertiary structure.
Annotate a DNA map of some type with terms from a controlled vocabulary.
Retrieve a phylogenetic tree from a data resource.
Data retrieval (protein interaction annotation)
Retrieve information on a protein interaction.
Data retrieval (protein family annotation)
Retrieve information on a protein family.
Retrieve information on a specific gene.
Data retrieval (genotype and phenotype annotation)
Genotype and phenotype information retrieval
Retrieve information on a specific genotype or phenotype.
Compare the architecture of two or more protein structures.
Identify the architecture of a protein structure.
Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.
Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).
Analyse a protein sequence (using methods that are only applicable to protein sequences).
Analyse known molecular tertiary structures.
Analyse nucleic acid tertiary structural data.
Process (read and / or write) a molecular secondary structure.
Compare two or more molecular tertiary structures.
Render a helical wheel representation of protein secondary structure.
Render a topology diagram of protein secondary structure.
Methods might identify structural neighbors, find structural similarities or define a structural core.
Secondary structure comparison (protein)
Protein subcellular localization prediction
Predict the subcellular localization of a protein sequence.
The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
Residue contact calculation (residue-residue)
Calculate contacts between residues in a protein structure.
Hydrogen bond calculation (inter-residue)
Identify potential hydrogen bonds between amino acid residues.
Predict the interactions of proteins with other molecules.
Process (read and / or write) codon usage data.
Process (read and / or write) gene expression (typically microarray) data.
Gene expression (microarray) data processing
Process (read and / or write) a network of gene regulation.
Analyse a known biological pathway or network.
Sequencing-based expression profile data analysis
Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts.
Analyse (e.g. characterize and model) alternative splicing events from comparing multiple nucleic acid sequences.
Process (read and / or write) nucleic acid sequence or structural data.
Process (read and / or write) protein sequence or structural data.
Process (read and / or write) molecular sequence data.
Process (read and / or write) molecular structural data.
Analyse a protein sequence alignment, typically to detect features or make predictions.
Sequence alignment analysis (nucleic acid)
Compare two or more nucleic acid sequences.
Back-translate a protein sequence into DNA.
Edit or change a nucleic acid sequence, either randomly or specifically.
Edit or change a protein sequence, either randomly or specifically.
Generate a nucleic acid sequence by some means.
Generate a protein sequence by some means.
Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
Visualise, format or render a nucleic acid sequence.
Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
Visualise, format or render a protein sequence.
Compare nucleic acid tertiary structures.
Process (read and / or write) nucleic acid tertiary structure data.
Generate a map of a DNA sequence annotated with positional or non-positional features of some type.
Process (read and / or write) a DNA map of some type.
Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information).
Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures.
Ligand-binding and active site prediction
Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits.
Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data.
Compare the physicochemical properties of two or more proteins (or reference data).
Compare two or more molecular secondary structures.
Generate a Hopp and Woods plot of antigenicity of a protein.
Microarray cluster textual view rendering
Visualise gene clusters with gene names.
Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis.
This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades.
Microarray cluster temporal graph rendering
Generate a dendrograph of raw, preprocessed or clustered microarray data.
Generate a plot of distances (distance matrix) between genes.
Microarray tree or dendrogram view rendering
Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression.
Microarray principal component rendering
Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values.
Generate a scatter plot of microarray data, typically after principal component analysis.
Visualise gene expression data where each band (or line graph) corresponds to a sample.
Visualise gene expression data after hierarchical clustering for representing hierarchical relationships.
Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.
Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.
For non-analytical operations, see the 'Processing' branch.
Apply analytical methods to existing data of a specific type.
Analyse an existing alignment of two or more molecular sequences, structures or derived data.
Analyse a body of scientific text (typically a full text article from a scientific journal.)
Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact.
Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions.
Calculate contacts between residues and some other group in a protein structure.
Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data.
Process (read and / or write) a molecular tertiary (3D) structure alignment.
Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc.
Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.
Process (read and / or write) molecular interaction data.
Assign molecular sequence(s) to a group or category.
Assign molecular structure(s) to a group or category.
Compare two or more proteins (or some aspect) to identify similarities.
Compare two or more nucleic acids to identify similarities.
Prediction, detection and recognition (protein)
Predict, recognise, detect or identify some properties of proteins.
Prediction, detection and recognition (nucleic acid)
Predict, recognise, detect or identify some properties of nucleic acids.
Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically.
Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically.
Render (visualise) a biological pathway or network.
Protein function prediction (from sequence)
Predict general (non-positional) functional properties of a protein from analysing its sequence.
name: Sequence motif recognition (protein)
Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.
Protein property calculation (from sequence)
Protein feature prediction (from structure)
Predict, recognise and identify positional features in proteins from analysing protein structure.
Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.
Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries.
Predict a network of protein interactions.
Design (or predict) nucleic acid sequences with specific chemical or physical properties.
Edit, convert or otherwise change a data entity, either randomly or specifically.
Evaluate a DNA sequence assembly, typically for purposes of quality control.
Align two or more (tpyically huge) molecular sequences that represent genomes.
Reconstruction of a sequence assembly in a localised area.
Render and visualise a DNA sequence assembly.
Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer.
The mapping of methylation sites in a DNA (genome) sequence.
Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.
Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced.
For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
Cut (remove) the end from a molecular sequence.
Compare the features of two genome sequences.
Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.
Detect errors in DNA sequences generated from sequencing projects).
Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.
Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.
Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.
A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation.
Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.
Operations usually score confidence in the prediction or some other statistical measure of evidence.
Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.
Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware.
Visualise, format or render an image of a Chromatogram.
Determine cytosine methylation states in nucleic acid sequences.
Determine cytosine methylation status of specific positions in a nucleic acid sequences.
Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay.
Methylation level analysis (gene-specific)
Many different techniques are available for this.
Measure the level of methyl cytosines in specific genes.
Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.
Compare the sequence or features of two or more genomes, for example, to find matching regions.
Generate an index of a genome sequence using the Burrows-Wheeler algorithm.
The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
A suffix array consists of the lexicographically sorted list of suffixes of a genome.
Generate an index of a genome sequence using a suffix arrays algorithm.
Analyse a spectrum from a mass spectrometry (or other) experiment.
Identify peaks in a spectrum from a mass spectrometry experiment.
Scaffold may be positioned along a chromosome physical map to create a "golden path".
Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps.
Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.
Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences.
Analyse raw sequence data from a sequencing pipeline and identify problems.
Pre-process sequence reads to ensure (or improve) quality and reliability.
This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples.
Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.
Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip').
Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
Differentially expressed gene identification
Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.
Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.
Gene sets can be defined beforehand by biological function, chromosome locations and so on.
Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)
Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.
Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.
Methods often utilise a database of aligned reads.
Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).
Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome.
Exome sequencing is considered a cheap alternative to whole genome sequencing.
Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications.
expression quantitative trait loci profiling
Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes.
Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.
Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).
Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products).
Infer a transcriptome sequence by analysis of short sequence reads.
Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other.
Infer a transcriptome sequence by mapping short reads to a reference genome.
Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc.
Calculate similarity between 2 or more documents.
Cluster (group) documents on the basis of their calculated similarity.
Recognise named entities (text tokens) within documents.
Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration.
Process data in such a way that makes it hard to trace to the person which the data concerns.
Search for and retrieve a data identifier of some kind, e.g. a database entry accession.
Generate a checksum of a molecular sequence.
Construct a bibliography from the scientific literature.
Predict the structure of a multi-subunit protein and particularly how the subunits fit together.
Analyse the surface properties of proteins.
Compare two or more ontologies, e.g. identify differences.
Analyse set(s) of terms from a controlled vocabulary to make scientific inferences.
'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.
Recognition of which format the given data is in.
The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs.
split a file containing multiple data items into many files, each containing one item
A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.
BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic.
GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials.
GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated.
Topic concerning the processing and analysis of nucleic acid sequence, structural and other data.
Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data.
This concept excludes macromolecules such as proteins and nucleic acids.
Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids.
Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.
This includes related concepts such as structural properties, alignments and structural motifs.
Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.
Topic concerning the prediction of molecular (secondary or tertiary) structure.
Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment).
BioCatalogue:Evolutionary Distance Measurements
This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.
Topic concerning the study of evolutionary relationships amongst organisms.
Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.
Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.
Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information.
This includes, for example, search, query and retrieval of molecular sequences and associated data.
This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation.
Topic concerning the archival, curation, processing and analysis of complex biological data.
Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data.
Topic concerning the study of the thermodynamic properties of a nucleic acid.
Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.
Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.
Topic concerning RNA sequences and structures.
Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids.
This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers.
Topic concerning the mapping of complete (typically nucleotide) sequences.
Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on.
Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell.
Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.
This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
Topic concerning the transcription of DNA into mRNA.
Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins).
Topic concerning the folding (in 3D space) of nucleic acid molecules.
Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion.
This includes the study of promoters, coding regions etc.
Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms.
Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues.
Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism.
Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.
Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.
This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
Topic concerning two-dimensional gel electrophoresis image and related data.
Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase.
Topic concerning protein microarray data.
Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein.
Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export.
Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence.
Use this concept for methods that are exclusively for protein structure.
Topic concerning the comparison of two or more protein structures.
The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures.
Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc.
Topic concerning protein-ligand (small molecule) interactions.
Topic concerning protein-DNA/RNA interactions.
Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
Topic concerning G-protein coupled receptors (GPCRs).
Topic concerning carbohydrates, typically including structural information.
Topic concerning lipids and their structures.
Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information.
Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included.
Edit, convert or otherwise change a molecular sequence, either randomly or specifically.
Sequence composition, complexity and repeats
Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.
Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites.
BioCatalogue:Protein Sequence Similarity
BioCatalogue:Nucleotide Sequence Similarity
The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
Topic concerning the comparison of two or more molecular sequences.
Topic concerning the archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
The query is a sequence-based entity such as another sequence, a motif or profile.
Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence).
Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities.
This includes systems that generate, process and analyse sequence clusters.
Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.
This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on.
The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment.
BioCatalogue:Protein Structure Prediction
Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features.
Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
BioCatalogue:Nucleotide Structure Prediction
BioCatalogue:Nucleotide Tertiary Structure
BioCatalogue:Nucleotide Secondary Structure
Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates.
Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data.
Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
This includes resources concerning flexibility and motion in protein and other molecular structures.
Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules.
Topic concerning the prediction of secondary or supersecondary structure of protein sequences.
Topic concerning the prediction of tertiary structure of protein sequences.
Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s).
For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments).
This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
BioCatalogue:Nucleotide Multiple Alignment
BioCatalogue:Nucleotide Pairwise Alignment
BioCatalogue:Nucleotide Sequence Alignment
This includes the generation, storage, analysis, rendering etc. of structure alignments.
Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment).
Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment.
Currently too specific for the topic sub-ontology (but might be unobsoleted).
Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree.
Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.
Topic concerning simulated polymerase chain reaction (PCR).
Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence.
This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.
Topic concerning DNA sequence variation (mutation and polymorphism) data.
Topic concerning microarrays, for example, to process microarray data or design probes and experiments.
Topic concerning the study of drugs and their effects or responses in living systems.
Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.
Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.
This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.
Topic concerning primarily the regulation of gene expression.
Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.
This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation.
Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation.
Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation.
The resource may be specific to a group of mice / rats or all mice / rats.
Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation.
The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query.
Topic concerning the analysis of the biomedical and informatics literature.
Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary.
This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on.
Topic concerning basic manipulations of files or reports of generic biological data.
Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.
Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
Topic concerning the classification of molecular sequences based on some measure of their similarity.
Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc.
Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type.
This includes comparison, discovery, recognition etc. of sequence motifs.
EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)
Topic concerning protein chemical modifications, e.g. post-translational modifications.
Molecular interactions, pathways and networks
Topic concerning molecular interactions, biological pathways, networks and other models.
A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area.
Data resources for the biological or biomedical literature, either a primary source of literature or some derivative.
Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.
Topic concerning general cell culture or data on a specific cell lines.
Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics).
Topic concerning the use of electrons to analyse structures at resolutions higher than can be achieved using light.
Topic concerning the cell cycle including key genes and proteins.
Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides.
Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome).
Topic concerning ribosomes, typically of ribosome-related genes and proteins.
Topic concerning the structures of drugs, drug target, their interactions and binding affinities.
Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology.
This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.
Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins.
Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.
Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc.
Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR).
This includes the design of primers for PCR and DNA amplification or the design of molecular probes.
Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.
Topic concerning a particular protein, protein family or other group of proteins.
Topic concerning organism classification, identification and naming.
Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles.
Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles.
BioCatalogue:Nucleotide Sequence Analysis
Topic concerning the repetitive nature of molecular sequences.
Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity.
Topic concerning a specific proteome including protein sequences and annotation.
The DNA sequences might be coding or non-coding sequences.
Topic concerning DNA sequences and structure, including processes such as methylation and replication.
Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences.
Functional, regulatory and non-coding RNA
Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).
Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).
Topic concerning one or more ribosomal RNA (rRNA) sequences.
Topic concerning one or more transfer RNA (tRNA) sequences.
This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
BioCatalogue:Protein Secondary Structure
Topic concerning protein secondary structure or secondary structure alignments.
Topic concerning RNA secondary or tertiary structure and alignments.
Topic concerning protein tertiary structures.
Topic concerning classification of nucleic acid sequences and structures.
A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.
Topic concerning protein tertiary structural domains and folds.
Topic concerning nucleotide sequence alignments.
Topic concerning protein sequence alignments.
Topic concerning the archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences.
Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites.
Transcription factors and regulatory sites
Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.
Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators.
Topic concerning protein phosphorylation and phosphorylation sites in protein sequences.
Topic concerning biological or biomedical analytical workflows or pipelines.
Topic concerning structuring data into basic types and (computational) objects.
Topic concerning mitochondria, typically of mitochondrial genes and proteins.
Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation.
The resource may be specific to a plant, a group of plants or all plants.
The resource may be specific to a virus, a group of viruses or all viruses.
Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.
The resource may be specific to a fungus, a group of fungi or all fungi.
Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.
Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to a pathogen, a group of pathogens or all pathogens.
Topic concerning Arabidopsis-specific data.
Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny.
Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes.
Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns.
Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease.
Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.
Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.
Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc.
This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen.
This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.
Topic concerning the comparison of two or more molecular structures.
This might involve comparison of secondary or tertiary (3D) structural information.
Topic concerning the study of gene and protein function including the prediction of functional properties of a protein.
Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.
The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
Topic concerning protein data resources.
Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
Topic concerning cells, such as key genes and proteins involved in the cell cycle.
Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships.
Topic concerning lipoproteins (protein-lipid assemblies).
Visualise a phylogeny, for example, render a phylogenetic tree.
Topic concerning the application of information technology to chemistry in biological research environment.
Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein.
This includes databases of models and methods to construct or analyse a model.
Topic concerning the application of statistical methods to biological problems.
Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure).
The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour.
Topic concerning the prediction of functional properties of a protein.
A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual.
Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs.
Predict transmembrane domains and topology in protein sequences.
Use this concept for methods that are exclusively for nucleic acid structures.
Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures.
Topic concerning the study of cancer, for example, genes and proteins implicated in cancer.
Topic concerning structural and associated data for toxic chemical substances.
A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool.
A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding.
Topic concerning biological nomenclature (naming), symbols and terminology.
Topic concerning the genes, gene variations and proteins involved in one or more specific diseases.
Topic concerning protein secondary or tertiary structural data and/or associated annotation.
Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general.
Informatics resource (typically a database) primarily focussed on genes.
Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation.
The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.
Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.
The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
Topic concerning protein secondary or tertiary structure alignments.
Topic concerning the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials.
Ontologies, nomenclature and classification
Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics.
This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
Topic concerning immunity-related genes, proteins and their ligands.
Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance.
Topic concerning toxins and the adverse effects of these chemical substances on living organisms.
Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously.
Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters.
Topic concerning gene regulatory networks.
Informatics resources dedicated to one or more specific diseases (not diseases in general).
Topic for the design of nucleic acid sequences with specific conformations.
Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes.
Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids.
Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation.
Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles.
Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles.
Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.
Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation.
Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet.
Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity.
This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
Topic concerning the study of genes, genetic variation and heredity in living organisms.
Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight).
Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow.
Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA).
Topic concerning the documentation of resources such as tools, services and databases and how to get help.
Topic concerning the structural and functional organisation of genes and other genetic elements.
Topic concerning the application of information technology to health, disease and biomedicine.
Topic concerning how organisms grow and develop.
Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage.
Topic concerning the form and function of the structures of living organisms.
Topic concerning the scientific literature, reference information and documentation.
Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on.
Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences.
Topic concerning the detection of positional features such as functional sites in nucleotide sequences.
Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites.
Topic for modelling biological systems in mathematical terms.
Topic concerning the acquisition and deposition of biological data.
Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins.
Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.
Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.
Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc.
Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.
Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data.
Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.
A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.
Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing.
Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions.
Topic concerning the protection of data, for example, patient health data.
Topic concerning biological samples and specimens.
Topic concerning chemical substances and physico-chemical processes and that occur within living organisms.
Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).
This includes sub-topics such as histone modification and DNA methylation.
Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.
Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.
Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors.
Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.
Topic concerning the functions of living organisms and their constituent parts.
Topic concerning the biology of microorganisms.
Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system.
Topic concerning the biology of parasites.
Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease.
Topic concerning the study of the nervous system and brain; its anatomy, physiology and function.
Topic concerning the the patterns, cause, and effect of disease within populations.
Topic concerning the use of physics to study biological system.
Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.
This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).
Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.
Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances.
Topic concerning the theory and practical use of computer systems.
Topic concerning the study of matter, space and time, and related concepts such as energy and force.
This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc.
Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons.
Topic concerning the structure and function of genes at a molecular level.
Topic concerning the study of respiratory system.
Topic concerning the study of metabolic diseases.
Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).
Topic concerning the study of rare diseases.
Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems.
Topic concerning the diseases and abnormalities of the heart and circulatory system.
Topic concerning the discovery and design of drugs or potential drug compounds.
Topic concerning repositories of biological samples, typically human, for basic biological and clinical research.
Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines.
Topic concerning collections of microbial cells including bacteria, yeasts and moulds.
Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.
Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA.
Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice.
Topic concerning collections of chemicals, typically for use in high-throughput screening experiments.
Topic concerning biological science that is (typically) performed in the context of medicine.
Topic concerning the identity of biological data and the mapping of entities in different databases.
Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity.
Topic concerning objective indicators of biological state often used to assess health, and determinate treatment.
Topic concerning the procedures used to conduct an experiment.
Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data.
Topic concerning the combination of data from different sources to provide users with a unified view of these data.
Topic concerning any matter, surface or construct that interacts with a biological system.
Topic concerning the use of synthetic chemistry to study and manipulate biological systems.
Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials.
Topic concerning the use of chemistry to create new compounds.
Topic concerning the process that leads from an original formulation of a computing problem to executable programs.
Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery.
Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect.
Topic concerning the study of how a drug interacts with the body.
Topic concerning the discovery, development and approval of medicines.
Topic concerning the safety (or lack) of drugs and other medical interventions.
Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines.
Pharmacovigilence concerns safety once a drug has gone to market.
Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.
Topic concerning the visual representation of an object.
Topic concerning the use of imaging techniques to understand biology.
Topic concerning the use of imaging techniques for clinical purposes for medical research.
Topic concerning the use of optical instruments to magnify the image of an object.
Topic concerning the use of animals and alternatives in experimental research.
Topic concerning the study of organisms in the ocean or brackish waters.
Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them.
Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices.
Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use.
Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines.
Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells.
Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life.
Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals.
Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering.
Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging.
Allergy, clinical immunology and immunotherapeutics.
Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement.
Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain.
Topic concerning anaesthesia and anaesthetics.
Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury.
Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails.
Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures.
Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat.
Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism.
Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases.
Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum.
Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management.
Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth.
Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile.
Topic concerning the branch of medicine that deals with the infectious diseases of the tropics.
Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident.
Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents.
Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine.
Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles.
Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents.
Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour.
Topic concerning the health of the reproductive processes, functions and systems at all stages of life.
Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance.
Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney.
Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health.
An obsolete concept (redefined in EDAM).
Needed for conversion to the OBO format.