Tool

Attribute: Tool Accessibility

Valid Value	Description	Ontology
Open Access	The resource is freely accessible to anyone without restriction.	Not available
Open Access (With Restrictions)	The resource is freely accessible, but with some conditions on use (e.g., registration, attribution, or non-commercial use requirements).	Not available
Restricted Access	Access to the resource is limited to specific users or requires approval, such as a data use agreement or account request.	Not available

Attribute: Tool Cost

Valid Value	Description	Ontology
Commercial	Software which you have to pay to access.	Not available
Free of Charge	The resource can be used at no monetary cost.	Not available
Free of Charge (With Restrictions)	The resource can be used at no monetary cost, but with some conditions (e.g., limited to academic/non-commercial use).	Not available

Attribute: Tool Input Data

Valid Value	Description	Ontology
Accession	A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.	EDAM:data_2091
Alignment	An alignment of molecular sequences, structures or profiles derived from them.	EDAM:data_1916
Biological Model ID	Identifier of a mathematical model, typically an entry from a database.	EDAM:data_1085
Biological Model Name	Name of a biological (mathematical) model.	EDAM:data_1170
Cell Line Name	The name of a cell line.	EDAM:data_2316
Cell Migration Track Image	An image from a cell migration track assay.	EDAM:data_3449
Cell Type Identifier	A unique identifier of a type or group of cells.	EDAM:data_2655
Cell Type Name	The name of a type or group of cells.	EDAM:data_2892
Cell Type Ontology ID	Cell type ontology concept ID.	EDAM:data_3238
Chromosome Name	Name of a chromosome.	EDAM:data_0987
Chromosome Report	A human-readable collection of information about a specific chromosome.	EDAM:data_0919
Clustered Expression Profiles	Groupings of expression profiles according to a clustering algorithm.	EDAM:data_3768
Codon Number	The number of a codon, for instance, at which a mutation is located.	EDAM:data_2216
Comparison Matrix	Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.	EDAM:data_0874
Compound Identifier	Identifier of an entry from a database of chemicals.	EDAM:data_1086
Compound Name	Unique name of a chemical compound.	EDAM:data_0990
Concentration	The concentration of a chemical compound.	EDAM:data_2140
Count Matrix	A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak).	EDAM:data_3917
DNA Sequence	A DNA sequence.	EDAM:data_3494
Data Index	An index of data of biological relevance.	EDAM:data_0955
Data Reference	Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.	EDAM:data_2093
Database Search Results	A report of hits from searching a database of some type.	EDAM:data_2080
Drug Identifier	Identifier of a drug.	EDAM:data_0993
Drug Name	Common name of a drug.	EDAM:data_2899
Drug Report	A human-readable collection of information about a specific drug.	EDAM:data_1696
Electronic Health Record	A human-readable systematic collection of patient (or population) health information in a digital format.	EDAM:data_3861
Enzyme Kinetics Data	Data concerning chemical reaction(s) catalysed by enzyme(s).	EDAM:data_2024
Experimental Measurement	Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.	EDAM:data_3108
Expression Data	Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.	EDAM:data_2603
GO-Term Enrichment Data	A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins.	EDAM:data_3754
Gene Expression Matrix	The final processed (normalised) data for a set of hybridisations in a microarray experiment.	EDAM:data_3112
Gene Expression Profile	Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.	EDAM:data_0928
Gene ID	A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.	EDAM:data_2295
Gene ID (NCBI)	An NCBI unique identifier of a gene.	EDAM:data_1027
Gene Identifier	An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.	EDAM:data_1025
Gene Name	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.	EDAM:data_2299
Gene Report	A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.	EDAM:data_0916
Gene Symbol	The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.	EDAM:data_1026
Gene Tree	A phylogenetic tree that is an estimate of the character's phylogeny.	EDAM:data_3271
Genetic Map	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.	EDAM:data_1278
Genotype/Phenotype Report	A human-readable collection of information about 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.	EDAM:data_0920
Heat Map	A graphical 2D tabular representation of expression data, typically derived from an omics experiment. A heat map is a table where rows and columns correspond to different features and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that...	EDAM:data_1636
Hidden Markov Model	A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences.	EDAM:data_1364
Hierarchy	Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.	EDAM:data_2589
Histogram	Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots.	EDAM:data_3905
Identifier	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).	EDAM:data_0842
Image	Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen.	EDAM:data_2968
Image Metadata	Any data concerning a specific biological or biomedical image.	EDAM:data_3546
Kinetic Model	Mathematical model of a network, that contains biochemical kinetics.	EDAM:data_3241
MRI Image	An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.	EDAM:data_3442
Map	A map of (typically one) DNA sequence annotated with positional or non-positional features.	EDAM:data_1274
Map Data	Data describing a molecular map (genetic or physical) or a set of such maps, including various attributes of, data extracted from or derived from the analysis of them, but excluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped.	EDAM:data_2019
Mass Spectrometry Data	Data concerning a mass spectrometry measurement.	EDAM:data_2536
Mass Spectrum	Spectra from mass spectrometry.	EDAM:data_0943
Mathematical Model	A biological model represented in mathematical terms.	EDAM:data_0950
Matrix	An array of numerical values.	EDAM:data_2082
Molecular Property	A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.	EDAM:data_2087
Molecular Simulation Data	Data coming from molecular simulations, computer "experiments" on model molecules.	EDAM:data_3842
Molecule Identifier	Name or other identifier of a molecule.	EDAM:data_0982
Molecule Name	Name of a specific molecule.	EDAM:data_0984
Morphology Parameter	Experimentally determined parameter of the morphology of an organism, e.g. size & shape.	EDAM:data_3723
Mutation ID	A unique identifier of a specific mutation catalogued in a database.	EDAM:data_2209
Not Applicable	No description provided	Not available
Nucleic Acid Identifier	Name or other identifier of a nucleic acid molecule.	EDAM:data_2119
Nucleic Acid Report	A human-readable collection of information about one or more specific nucleic acid molecules.	EDAM:data_2084
Nucleic Acid Sequence	One or more nucleic acid sequences, possibly with associated annotation.	EDAM:data_2977
Ontology	An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.	EDAM:data_0582
Ontology Concept Data	Data concerning or derived from a concept from a biological ontology.	EDAM:data_0967
Ontology Data	Data concerning or derived from an ontology.	EDAM:data_2353
Ontology Identifier	Any arbitrary identifier of an ontology.	EDAM:data_2338
Ontology Mapping	A mapping of supplied textual terms or phrases to ontology concepts (URIs).	EDAM:data_3509
Ontology Name	Name of an ontology of biological or bioinformatics concepts and relations.	EDAM:data_1051
Ontology Term	A term (name) from an ontology.	EDAM:data_0966
Organism Identifier	A unique identifier of a (group of) organisms.	EDAM:data_1869
Organism Name	The name of an organism (or group of organisms).	EDAM:data_2909
Over-Represesntation Data	A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data.	EDAM:data_3753
P-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.	EDAM:data_1669
Pair Sequence Alignment	Alignment of exactly two molecular sequences.	EDAM:data_1381
Pathway Or Network	Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).	EDAM:data_2600
Pathway Or Network Report	An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.	EDAM:data_2984
Pathway Overrepresentation Data	A ranked list of pathways, each associated with z-score, p-value or similar, concerning or derived from the analysis of e.g. a set of genes or proteins.	EDAM:data_3953
Peptide Identification	Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer.	EDAM:data_0945
Peptide Property	Data concerning small peptides.	EDAM:data_2979
Phenotype Name	Name of a phenotype.	EDAM:data_3275
Phylogenetic Data	Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.	EDAM:data_2523
Phylogenetic Tree	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.	EDAM:data_0872
Plain Text	Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.	EDAM:data_3671
Plot	Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph.	EDAM:data_2884
Position Weight Matrix	A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.	EDAM:data_1362
Position-Specific Scoring Matrix	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.	EDAM:data_2854
Protein Contact Map	An amino acid residue contact map for a protein structure.	EDAM:data_1547
Protein Identifier	Identifier of a protein.	EDAM:data_0989
Protein Interaction Data	Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water,...	EDAM:data_0906
Protein Name	Name of a protein.	EDAM:data_1009
Protein Property	A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.	EDAM:data_0897
Protein Report	An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.	EDAM:data_0896
Protein Sequence	One or more protein sequences, possibly with associated annotation.	EDAM:data_2976
Protein Structure Report	A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains.	EDAM:data_1537
Quality Control Report	Report of the quality control review that was made of factors involved in a procedure.	EDAM:data_3914
RNA Sequence	An RNA sequence.	EDAM:data_3495
Raw Image	Raw biological or biomedical image generated by some experimental technique.	EDAM:data_3424
Reaction Data	Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.	EDAM:data_2978
RefSeq Accession	Accession number of a RefSeq database entry.	EDAM:data_1098
Report	A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the...	EDAM:data_2048
Resource Metadata	Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing.	EDAM:data_2337
Sample Annotation	Annotation on a biological sample, for example experimental factors and their values.	EDAM:data_3113
Sample ID	Name or other identifier of an entry from a biosample database.	EDAM:data_3273
Score	A numerical value, that is some type of scored value arising for example from a prediction method.	EDAM:data_1772
Sequence	One or more molecular sequences, possibly with associated annotation.	EDAM:data_2044
Sequence Alignment	Alignment of multiple molecular sequences.	EDAM:data_0863
Sequence Attribute	An attribute of a molecular sequence, possibly in reference to some other sequence.	EDAM:data_2534
Sequence Cluster	A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.	EDAM:data_1235
Sequence Composition Plot	A plot of character or word composition / frequency of a molecular sequence.	EDAM:data_2166
Sequence Composition Report	A report (typically a table) on character or word composition / frequency of a molecular sequence(s).	EDAM:data_1261
Sequence Coordinates	A position in a map (for example a genetic map), either a single position (point) or a region / interval.	EDAM:data_2012
Sequence Features	Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.	EDAM:data_1255
Sequence Image	Image of a molecular sequence, possibly with sequence features or properties shown.	EDAM:data_2969
Sequence Motif	Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.	EDAM:data_1353
Sequence Position	A position of one or more points (base or residue) in a sequence, or part of such a specification.	EDAM:data_1016
Sequence Property	An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.	EDAM:data_1254
Sequence Range	Specification of range(s) of sequence positions.	EDAM:data_1017
Sequence Record	A molecular sequence and associated metadata.	EDAM:data_0849
Sequence Report	An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.	EDAM:data_2955
Sequence Search Results	A report of sequence hits and associated data from searching a database of sequences (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.	EDAM:data_0857
Sequence Set	A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.	EDAM:data_0850
Sequence Signature Data	Sequence signature data concerns specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.	EDAM:data_0860
Sequence Similarity	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.	EDAM:data_1413
Sequence Similarity Score	A value representing molecular sequence similarity.	EDAM:data_0865
Sequence Variations	Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.	EDAM:data_3498
Simulation	Data coming from molecular simulations, computer "experiments" on model molecules. Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).	EDAM:data_3869
Small Molecule Report	A human-readable collection of information about a specific chemical compound.	EDAM:data_0962
Spectrum	The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.	EDAM:data_3483
Statistical Estimate Score	A value representing estimated statistical significance of some observed data; typically sequence database hits.	EDAM:data_0951
Strain Identifier	Identifier of a strain of an organism variant, typically a plant, virus or bacterium.	EDAM:data_2379
Strain Name	The name of a strain of an organism variant, typically a plant, virus or bacterium.	EDAM:data_1046
Structure	3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.	EDAM:data_0883
Structure Report	A human-readable collection of information about one or more molecular tertiary (3D) structures. It might include annotation on the structure, a computer-generated report of analysis of structural data, and metadata (data about primary data) or any other free (essentially unformatted) text, as...	EDAM:data_2085
Taxonomy	Data concerning the classification, identification and naming of organisms.	EDAM:data_3028
Text Data	Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.	EDAM:data_2526
Text Mining Report	A human-readable collection of information resulting from text mining.	EDAM:data_0972
Topology Data	Static information of a structure molecular system that is needed for a molecular simulation: the list of atoms, their non-bonded parameters for Van der Waals and electrostatic interactions, and the complete connectivity in terms of bonds, angles and dihedrals.	EDAM:data_3872
Training Material	Learning material is a document or another digital object that is designed for learning (educational, training) purposes.	EDAM:data_3669
Trajectory Data	Dynamic information of a structure molecular system coming from a molecular simulation: XYZ 3D coordinates (sometimes with their associated velocities) for every atom along time.	EDAM:data_3870
Transcription Factor Identifier	Identifier of a transcription factor (or a TF binding site).	EDAM:data_1077
Transcription Factor Name	The name of a transcription factor.	EDAM:data_2755
Vmax	The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.	EDAM:data_0909
dbSNP ID	Identifier of a dbSNP database entry.	EDAM:data_1106

Attribute: Tool Output Data

Valid Value	Description	Ontology
Accession	A persistent (stable) and unique identifier, typically identifying an object (entry) from a database.	EDAM:data_2091
Alignment	An alignment of molecular sequences, structures or profiles derived from them.	EDAM:data_1916
Biological Model ID	Identifier of a mathematical model, typically an entry from a database.	EDAM:data_1085
Biological Model Name	Name of a biological (mathematical) model.	EDAM:data_1170
Cell Line Name	The name of a cell line.	EDAM:data_2316
Cell Migration Track Image	An image from a cell migration track assay.	EDAM:data_3449
Cell Type Identifier	A unique identifier of a type or group of cells.	EDAM:data_2655
Cell Type Name	The name of a type or group of cells.	EDAM:data_2892
Cell Type Ontology ID	Cell type ontology concept ID.	EDAM:data_3238
Chromosome Name	Name of a chromosome.	EDAM:data_0987
Chromosome Report	A human-readable collection of information about a specific chromosome.	EDAM:data_0919
Clustered Expression Profiles	Groupings of expression profiles according to a clustering algorithm.	EDAM:data_3768
Codon Number	The number of a codon, for instance, at which a mutation is located.	EDAM:data_2216
Comparison Matrix	Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison.	EDAM:data_0874
Compound Identifier	Identifier of an entry from a database of chemicals.	EDAM:data_1086
Compound Name	Unique name of a chemical compound.	EDAM:data_0990
Concentration	The concentration of a chemical compound.	EDAM:data_2140
Count Matrix	A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak).	EDAM:data_3917
DNA Sequence	A DNA sequence.	EDAM:data_3494
Data Index	An index of data of biological relevance.	EDAM:data_0955
Data Reference	Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology.	EDAM:data_2093
Database Search Results	A report of hits from searching a database of some type.	EDAM:data_2080
Drug Identifier	Identifier of a drug.	EDAM:data_0993
Drug Name	Common name of a drug.	EDAM:data_2899
Drug Report	A human-readable collection of information about a specific drug.	EDAM:data_1696
Electronic Health Record	A human-readable systematic collection of patient (or population) health information in a digital format.	EDAM:data_3861
Enzyme Kinetics Data	Data concerning chemical reaction(s) catalysed by enzyme(s).	EDAM:data_2024
Experimental Measurement	Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.	EDAM:data_3108
Expression Data	Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.	EDAM:data_2603
GO-Term Enrichment Data	A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins.	EDAM:data_3754
Gene Expression Matrix	The final processed (normalised) data for a set of hybridisations in a microarray experiment.	EDAM:data_3112
Gene Expression Profile	Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments.	EDAM:data_0928
Gene ID	A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.	EDAM:data_2295
Gene ID (NCBI)	An NCBI unique identifier of a gene.	EDAM:data_1027
Gene Identifier	An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.	EDAM:data_1025
Gene Name	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.	EDAM:data_2299
Gene Report	A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.	EDAM:data_0916
Gene Symbol	The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name.	EDAM:data_1026
Gene Tree	A phylogenetic tree that is an estimate of the character's phylogeny.	EDAM:data_3271
Genetic Map	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.	EDAM:data_1278
Genotype/Phenotype Report	A human-readable collection of information about 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.	EDAM:data_0920
Heat Map	A graphical 2D tabular representation of expression data, typically derived from an omics experiment. A heat map is a table where rows and columns correspond to different features and contexts (for example, cells or samples) and the cell colour represents the level of expression of a gene that...	EDAM:data_1636
Hidden Markov Model	A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences.	EDAM:data_1364
Hierarchy	Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation.	EDAM:data_2589
Histogram	Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots.	EDAM:data_3905
Identifier	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).	EDAM:data_0842
Image	Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen.	EDAM:data_2968
Image Metadata	Any data concerning a specific biological or biomedical image.	EDAM:data_3546
Kinetic Model	Mathematical model of a network, that contains biochemical kinetics.	EDAM:data_3241
MRI Image	An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body.	EDAM:data_3442
Map	A map of (typically one) DNA sequence annotated with positional or non-positional features.	EDAM:data_1274
Map Data	Data describing a molecular map (genetic or physical) or a set of such maps, including various attributes of, data extracted from or derived from the analysis of them, but excluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped.	EDAM:data_2019
Mass Spectrometry Data	Data concerning a mass spectrometry measurement.	EDAM:data_2536
Mass Spectrum	Spectra from mass spectrometry.	EDAM:data_0943
Mathematical Model	A biological model represented in mathematical terms.	EDAM:data_0950
Matrix	An array of numerical values.	EDAM:data_2082
Molecular Property	A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule.	EDAM:data_2087
Molecular Simulation Data	Data coming from molecular simulations, computer "experiments" on model molecules.	EDAM:data_3842
Molecule Identifier	Name or other identifier of a molecule.	EDAM:data_0982
Molecule Name	Name of a specific molecule.	EDAM:data_0984
Morphology Parameter	Experimentally determined parameter of the morphology of an organism, e.g. size & shape.	EDAM:data_3723
Mutation ID	A unique identifier of a specific mutation catalogued in a database.	EDAM:data_2209
Not Applicable	No description provided	Not available
Nucleic Acid Identifier	Name or other identifier of a nucleic acid molecule.	EDAM:data_2119
Nucleic Acid Report	A human-readable collection of information about one or more specific nucleic acid molecules.	EDAM:data_2084
Nucleic Acid Sequence	One or more nucleic acid sequences, possibly with associated annotation.	EDAM:data_2977
Ontology	An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.	EDAM:data_0582
Ontology Concept Data	Data concerning or derived from a concept from a biological ontology.	EDAM:data_0967
Ontology Data	Data concerning or derived from an ontology.	EDAM:data_2353
Ontology Identifier	Any arbitrary identifier of an ontology.	EDAM:data_2338
Ontology Mapping	A mapping of supplied textual terms or phrases to ontology concepts (URIs).	EDAM:data_3509
Ontology Name	Name of an ontology of biological or bioinformatics concepts and relations.	EDAM:data_1051
Ontology Term	A term (name) from an ontology.	EDAM:data_0966
Organism Identifier	A unique identifier of a (group of) organisms.	EDAM:data_1869
Organism Name	The name of an organism (or group of organisms).	EDAM:data_2909
Over-Represesntation Data	A ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data.	EDAM:data_3753
P-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.	EDAM:data_1669
Pair Sequence Alignment	Alignment of exactly two molecular sequences.	EDAM:data_1381
Pathway Or Network	Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).	EDAM:data_2600
Pathway Or Network Report	An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation.	EDAM:data_2984
Pathway Overrepresentation Data	A ranked list of pathways, each associated with z-score, p-value or similar, concerning or derived from the analysis of e.g. a set of genes or proteins.	EDAM:data_3953
Peptide Identification	Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer.	EDAM:data_0945
Peptide Property	Data concerning small peptides.	EDAM:data_2979
Phenotype Name	Name of a phenotype.	EDAM:data_3275
Phylogenetic Data	Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees.	EDAM:data_2523
Phylogenetic Tree	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.	EDAM:data_0872
Plain Text	Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.	EDAM:data_3671
Plot	Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph.	EDAM:data_2884
Position Weight Matrix	A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position.	EDAM:data_1362
Position-Specific Scoring Matrix	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.	EDAM:data_2854
Protein Contact Map	An amino acid residue contact map for a protein structure.	EDAM:data_1547
Protein Identifier	Identifier of a protein.	EDAM:data_0989
Protein Interaction Data	Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water,...	EDAM:data_0906
Protein Name	Name of a protein.	EDAM:data_1009
Protein Property	A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.	EDAM:data_0897
Protein Report	An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data.	EDAM:data_0896
Protein Sequence	One or more protein sequences, possibly with associated annotation.	EDAM:data_2976
Protein Structure Report	A human-readable collection of information about one or more specific protein 3D structure(s) or structural domains.	EDAM:data_1537
Quality Control Report	Report of the quality control review that was made of factors involved in a procedure.	EDAM:data_3914
RNA Sequence	An RNA sequence.	EDAM:data_3495
Raw Image	Raw biological or biomedical image generated by some experimental technique.	EDAM:data_3424
Reaction Data	Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction.	EDAM:data_2978
RefSeq Accession	Accession number of a RefSeq database entry.	EDAM:data_1098
Report	A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the...	EDAM:data_2048
Resource Metadata	Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing.	EDAM:data_2337
Sample Annotation	Annotation on a biological sample, for example experimental factors and their values.	EDAM:data_3113
Sample ID	Name or other identifier of an entry from a biosample database.	EDAM:data_3273
Score	A numerical value, that is some type of scored value arising for example from a prediction method.	EDAM:data_1772
Sequence	One or more molecular sequences, possibly with associated annotation.	EDAM:data_2044
Sequence Alignment	Alignment of multiple molecular sequences.	EDAM:data_0863
Sequence Attribute	An attribute of a molecular sequence, possibly in reference to some other sequence.	EDAM:data_2534
Sequence Cluster	A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.	EDAM:data_1235
Sequence Composition Plot	A plot of character or word composition / frequency of a molecular sequence.	EDAM:data_2166
Sequence Composition Report	A report (typically a table) on character or word composition / frequency of a molecular sequence(s).	EDAM:data_1261
Sequence Coordinates	A position in a map (for example a genetic map), either a single position (point) or a region / interval.	EDAM:data_2012
Sequence Features	Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.	EDAM:data_1255
Sequence Image	Image of a molecular sequence, possibly with sequence features or properties shown.	EDAM:data_2969
Sequence Motif	Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence.	EDAM:data_1353
Sequence Position	A position of one or more points (base or residue) in a sequence, or part of such a specification.	EDAM:data_1016
Sequence Property	An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis.	EDAM:data_1254
Sequence Range	Specification of range(s) of sequence positions.	EDAM:data_1017
Sequence Record	A molecular sequence and associated metadata.	EDAM:data_0849
Sequence Report	An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties.	EDAM:data_2955
Sequence Search Results	A report of sequence hits and associated data from searching a database of sequences (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.	EDAM:data_0857
Sequence Set	A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.	EDAM:data_0850
Sequence Signature Data	Sequence signature data concerns specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element.	EDAM:data_0860
Sequence Similarity	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.	EDAM:data_1413
Sequence Similarity Score	A value representing molecular sequence similarity.	EDAM:data_0865
Sequence Variations	Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.	EDAM:data_3498
Simulation	Data coming from molecular simulations, computer "experiments" on model molecules. Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).	EDAM:data_3869
Small Molecule Report	A human-readable collection of information about a specific chemical compound.	EDAM:data_0962
Spectrum	The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment.	EDAM:data_3483
Statistical Estimate Score	A value representing estimated statistical significance of some observed data; typically sequence database hits.	EDAM:data_0951
Strain Identifier	Identifier of a strain of an organism variant, typically a plant, virus or bacterium.	EDAM:data_2379
Strain Name	The name of a strain of an organism variant, typically a plant, virus or bacterium.	EDAM:data_1046
Structure	3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.	EDAM:data_0883
Structure Report	A human-readable collection of information about one or more molecular tertiary (3D) structures. It might include annotation on the structure, a computer-generated report of analysis of structural data, and metadata (data about primary data) or any other free (essentially unformatted) text, as...	EDAM:data_2085
Taxonomy	Data concerning the classification, identification and naming of organisms.	EDAM:data_3028
Text Data	Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.	EDAM:data_2526
Text Mining Report	A human-readable collection of information resulting from text mining.	EDAM:data_0972
Topology Data	Static information of a structure molecular system that is needed for a molecular simulation: the list of atoms, their non-bonded parameters for Van der Waals and electrostatic interactions, and the complete connectivity in terms of bonds, angles and dihedrals.	EDAM:data_3872
Training Material	Learning material is a document or another digital object that is designed for learning (educational, training) purposes.	EDAM:data_3669
Trajectory Data	Dynamic information of a structure molecular system coming from a molecular simulation: XYZ 3D coordinates (sometimes with their associated velocities) for every atom along time.	EDAM:data_3870
Transcription Factor Identifier	Identifier of a transcription factor (or a TF binding site).	EDAM:data_1077
Transcription Factor Name	The name of a transcription factor.	EDAM:data_2755
Vmax	The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large.	EDAM:data_0909
dbSNP ID	Identifier of a dbSNP database entry.	EDAM:data_1106

Attribute: Tool Documentation Type

Valid Value	Description	Ontology
API Documentation	Documentation describing the tool's application programming interface (API), including available endpoints/functions and how to use them.	schema:APIReference
Citation Instructions	Documentation describing how the tool should be cited in publications.	EDAM:data_0970
Code of Conduct	Documentation describing expected behavior and community standards for contributors and users of the tool.	Not available
Command-Line Options	Documentation describing the tool's command-line arguments and flags.	Not available
Contributions Policy	Documentation describing how external contributors can propose changes or additions to the tool.	Not available
FAQ	Frequently Asked Questions (and answers) about the software.	schema:FAQPage
General	General documentation.	Not available
Governance	Information about the software governance model.	Not available
Installation Instructions	Documentation describing how to install or set up the tool.	Not available
Other	Some other type of documentation not listed in biotoolsSchema.	Not available
Quick Start Guide	Documentation providing a brief introduction to get a new user running the tool quickly.	Not available
Release Notes	Documentation describing changes, fixes, and new features introduced in each version of the tool.	Not available
Terms of Use	Documentation describing the legal terms and conditions governing use of the tool.	Not available
Training Material	Documentation or resources designed to teach users how to use the tool, such as tutorials or workshop materials.	EDAM:data_3669
User Manual	Comprehensive documentation describing how to use all of the tool's features.	Not available

Attribute: Tool Download Type

Valid Value	Description	Ontology
API Specification	A formal specification (e.g., OpenAPI/Swagger) describing the tool's API, made available for download.	Not available
Binaries	Binaries for the software; compiled code that allow a program to be installed without having to compile the source code.	NCIT:C190168
Biological Data	Biological data files (e.g., reference datasets) distributed alongside the tool.	SIO:010019
Command-Line Specification	A formal specification of the tool's command-line interface, made available for download.	Not available
Container File	A containerized version of the tool (e.g., a Docker or Singularity image), made available for download.	Not available
Downloads Page	A web page listing available downloads for the tool.	Not available
Icon	Icon of the software.	Not available
Other	Other type of download for software - the default if a more specific type is not available.	Not available
Screenshot	Screenshot of the software.	schema:screenshot
Software Package	A packaged, installable distribution of the tool (e.g., a pip/conda/CRAN package).	Not available
Source Code	The tool's raw source code, made available for download (e.g., via a code repository).	NCIT:C47901
Test Data	Sample or test datasets distributed alongside the tool for validation or demonstration purposes.	Not available
Test Script	A script provided to test or validate a tool installation.	Not available
Tool Wrapper (CWL)	A Common Workflow Language (CWL) wrapper enabling the tool to be run as part of a CWL-based workflow.	Not available
Tool Wrapper (Galaxy)	A Galaxy tool wrapper enabling the tool to be run within the Galaxy platform.	Not available
Tool Wrapper (Taverna)	A Taverna workflow wrapper enabling the tool to be run within the Taverna platform.	Not available
Tool wrapper (Other)	A workflow-engine wrapper for the tool, for a platform other than CWL, Galaxy, or Taverna.	Not available
VM Image	A virtual machine image with the tool pre-installed, made available for download.	Not available

Attribute: Tool Input Format

Valid Value	Description	Ontology
Alignment Format	Data format for molecular sequence alignment information.	EDAM:format_1921
Alignment Format (Pair Only)	Data format for molecular sequence alignment information that can hold the alignment of only two sequences.	EDAM:format_2920
Alignment Format (Text)	Text-based format for molecular sequence alignment information.	EDAM:format_2554
Annotated Text Format	Data format of an annotated text, e.g. with recognised entities, concepts, and relations.	EDAM:format_3780
Antimony	A human-readable, text-based modeling language for specifying systems biology models (reaction networks, rate laws, and initial conditions) that can be compiled to SBML; used by tools such as Tellurium/libAntimony.	Not available
BAM	BAM format, the binary, BGZF-compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to a reference sequence; may contain base-call and alignment qualities and other data.	EDAM:format_2572
BCF	The binary version of Variant Call Format (VCF) used to store sequence variation data such as indels, polymorphisms, and structural variants.	EDAM:format_3020
BED	Browser Extensible Data (BED) format for sequence annotation tracks, typically displayed in a genome browser.	EDAM:format_3003
BLAST Results	Format of results from a sequence database search using some variant of BLAST, including score data, alignment data, and summary tables.	EDAM:format_1333
BNGL	BioNetGen Language (BNGL), a format for specifying and simulating rule-based models of biochemical systems such as signal transduction, metabolic, and genetic regulatory networks.	EDAM:format_3972
Binary Format	A generic format in which data is encoded as binary, machine-readable content rather than plain text.	EDAM:format_2333
Biological Model Format	A category of formats used to encode computational or mathematical models of biological systems and processes, such as reaction networks or systems biology models.	EDAM:format_2013
Biological Pathway Or Network Format	Data format for representing a biological pathway or network.	EDAM:format_2013
CSV	Tabular data represented as comma-separated values in a text file.	EDAM:format_3752
Chemical Data Format	Format of a report on a chemical compound or other chemical data.	EDAM:format_2030
Cytoband Format	Format for chromosome cytoband data, reflecting a UCSC Genome Browser database table.	EDAM:format_3235
Cytoscape Input File Format	Format of the Cytoscape input file in which gene expression ratios or values are specified over one or more experiments.	EDAM:format_3477
DCC	A tab-delimited count file produced by the NanoString GeoMx Digital Spatial Profiler, containing per-probe digital count data for a given region of interest.	Not available
DCD	A binary trajectory file format used by molecular dynamics simulation packages such as CHARMM and NAMD to store atomic coordinates (and optionally velocities) over the course of a simulation.	Not available
DSV	Tabular data represented as values delimited by some (non-comma, non-tab) character in a text file.	EDAM:format_3751
Database Hits (Sequence) Format	Format of a report on sequence hits and associated data from searching a sequence database.	EDAM:format_2066
Docker Image Format	A Docker image is a file, comprised of multiple layers, used to execute code in a Docker container; it packages an application together with its dependencies for a complete, executable environment.	EDAM:format_3973
Document Format	Format of documents, including word processor, spreadsheet, and presentation files.	EDAM:format_3507
Dot-Bracket Format	Format for RNA secondary structure using dot-bracket notation, originally generated by the Vienna RNA package/server.	EDAM:format_1457
FASTA	Text-based format for representing nucleotide or peptide sequences, in which each sequence is preceded by a single-line description starting with a '>' character.	EDAM:format_1929
FASTQ	Text-based format for storing both a biological sequence (usually nucleotide) and its corresponding quality scores, most commonly used for raw sequencing reads.	EDAM:format_1930
FASTQ-Illumina	FASTQ short read format variant using the Illumina 1.3+ quality-score encoding scheme.	EDAM:format_1931
FCS	Flow Cytometry Standard (FCS), the standard binary file format for storing multiparameter flow or mass cytometry data produced by cytometry instruments.	OBI:0000327
GCT/Res Format	Tab-delimited text file format (used by GenePattern) containing a column for each sample, a row for each gene, and an expression value for each gene in each sample.	EDAM:format_3709
GFF	General/Generic Feature Format (GFF) for describing genes and other sequence features, of indeterminate version.	EDAM:format_2305
GFF3	Generic Feature Format version 3 (GFF3), a tab-delimited format for describing genomic features with a well-defined hierarchy of parent-child relationships.	EDAM:format_1975
GIF	Graphics Interchange Format, a bitmap image format supporting compression and animation.	EDAM:format_3467
GML	Graph Modeling Language (GML), a plain-text format for describing graph/network data, used by tools such as Cytoscape, Pajek, yEd, and NetworkX.	EDAM:format_3822
GTF	Gene Transfer Format (GTF), a restricted, more strictly-defined version of GFF used to describe gene structure annotations.	EDAM:format_2306
Gene Annotation Format	Format of a report on a particular locus, gene, gene system, or group of genes.	EDAM:format_2031
Gene Cluster Format	A tab-delimited matrix file format that describes a gene expression dataset, where columns correspond to samples/profiles, rows correspond to genes, and cell values correspond to expression measurements.	NCIT:C123891
Gene Expression Report Format	Format of a file of gene expression data, such as a gene expression matrix or profile.	EDAM:format_2058
Genotype And Phenotype Annotation Format	A category of formats used to represent annotations linking genotype data to associated phenotype information, e.g. from studies or databases such as dbGaP.	Not available
Graph Format	Data format for representing graph data, i.e. a set of nodes and the edges connecting them.	EDAM:format_3617
H5AD	HDF5-based binary file format used by the AnnData Python library to store annotated data matrices (e.g. gene expression matrices with associated cell/feature metadata), widely used in single-cell genomics tools such as Scanpy.	Not available
HDF	Hierarchical Data Format (HDF), a set of file formats and libraries for storing and organizing large amounts of numerical data.	EDAM:format_3873
HDF5	HDF5, the current version of the Hierarchical Data Format; a data model, library, and file format for storing and managing large, complex, heterogeneous data.	EDAM:format_3590
HTML	HyperText Markup Language (HTML) format, used for structuring and rendering documents on the web.	EDAM:format_2331
Hidden Markov Model Format	Format for representing a hidden Markov model, e.g. as used for sequence profile searching.	EDAM:format_2072
Image Format	A generic category of formats used for images and associated image metadata.	EDAM:format_3547
Individual Genetic Data Format	Format for metadata describing an individual along with their associated genetic data.	EDAM:format_3287
JPG	Joint Photographic Experts Group (JPEG) format, a common lossy compressed image format.	EDAM:format_3579
JSON	JavaScript Object Notation (JSON), a lightweight, text-based format for representing tree-structured data using key-value pairs.	EDAM:format_3464
LSM	Zeiss' proprietary microscopy image format (based on TIFF), the default data export format for Zeiss LSM-series confocal microscopes, containing image data plus imaging acquisition settings.	EDAM:format_3988
MAF	Mutation Annotation Format (MAF), a tab-delimited text file that aggregates mutation/variant information across a set of samples from one or more VCF files, commonly used in cancer genomics.	NCIT:C172215
MAGE-ML	MAGE-ML, an XML-based format standardized by MGED (now FGED) for representing microarray gene expression data.	EDAM:format_3161
MAGE-TAB	MAGE-TAB, a tab-delimited textual format standardized by MGED (now FGED) for representing microarray gene expression data.	EDAM:format_3162
MAT	A proprietary, binary data container format used by MATLAB software to store workspace variables.	NCIT:C190178
MATLAB Script	File format for scripts or functions written in the MATLAB programming language.	EDAM:format_4007
MSF	A structured (SQLite-based) mass spectrometry result file format used by Thermo Scientific's Proteome Discoverer software.	EDAM:format_3702
Map Format	A format used to encode a genetic or physical map, specifying the positions and/or order of markers such as SNPs or genes along a chromosome (e.g. PLINK MAP files).	EDAM:format_2060
Mass Spectrometry Data Format	Format for mass spectra and derived data, including peptide sequences and related metadata.	EDAM:format_3245
Matrix Format	Format of a matrix (array) of numerical values.	EDAM:format_3033
NIFTI Format	An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI), commonly used to store brain imaging data obtained via Magnetic Resonance Imaging (MRI).	EDAM:format_3549
Nexus Format	Phylogenetic tree Nexus (text) format, used to store aligned sequences and/or tree data along with associated metadata blocks.	EDAM:format_1912
Not Applicable	Placeholder value used when specifying a tool input/output format is not applicable to the entry being described.	Not available
NumPy Format	The standard binary file format used by NumPy - a fundamental Python package for scientific computing - for persisting a single arbitrary NumPy array on disk, including its shape and dtype information.	EDAM:format_4003
OME-TIFF	Open Microscopy Environment TIFF (OME-TIFF), an image file format consisting of standard TIFF/BigTIFF data with OME-XML metadata embedded in the image description, used to store microscopy image data.	EDAM:format_3727
Ontology Format	A generic category of formats used for representing ontologies.	EDAM:format_2195
PDF	Portable Document Format (PDF), a fixed-layout document format for reliably presenting text, images, and formatting independent of application, hardware, or operating system.	EDAM:format_3508
PNG	Portable Network Graphics (PNG), a lossless bitmap image compression format intended to replace GIF.	EDAM:format_3603
PS	PostScript format, a page description language used for representing formatted printable or displayable documents and vector graphics.	EDAM:format_3696
PSF	Protein Structure File (PSF), a structure topology file format used by NAMD and CHARMM molecular simulation programs, containing atoms, bonds, angles, dihedrals, and related force-field terms.	EDAM:format_3882
Phylip Format	PHYLIP format for (aligned) molecular sequences, used by the PHYLIP phylogenetics software package.	EDAM:format_1997
Phylip Format Variant	Some non-standard variant of PHYLIP format for (aligned) sequences.	EDAM:format_2924
Phylogenetic Tree Format	Data format for representing a phylogenetic tree.	EDAM:format_2006
Phylogenetic Tree Format (Text)	Text-based format for representing a phylogenetic tree.	EDAM:format_2556
Protein Interaction Format	Format for molecular (protein-protein) interaction data.	EDAM:format_2054
Python Script	File format for scripts written in Python, a widely used high-level, general-purpose programming language.	EDAM:format_3996
R File Format	File format used for scripts written in the R programming language, executed within the R software environment for statistical computation and graphics.	EDAM:format_3554
R Script	Format for scripts written in the R language, an open-source programming language and environment for statistical computing and graphics.	EDAM:format_3999
RDS	A native binary file format used by R to save and load a single serialized R object to and from a file.	NCIT:C209895
RNA Annotation Format	A general category of formats for annotated RNA data, including e.g. microRNA and RNA-Seq data.	EDAM:format_3865
RNA Secondary Structure Format	Format for the (predicted or experimentally determined) secondary structure of an RNA molecule.	EDAM:format_2076
RPKM	Tab-delimited format for a gene expression levels table, with values calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).	EDAM:format_3980
Raw Sequence Format	Format of a raw molecular sequence, i.e. specifying only the alphabet/characters used with no additional annotation.	EDAM:format_2571
SAM	Sequence Alignment/Map (SAM) format, a text-based format for storing alignments of nucleotide sequences (e.g. sequencing reads) to a reference sequence, including base-call and alignment qualities.	EDAM:format_2573
SBML	Systems Biology Markup Language (SBML), the standard XML format for encoding models of biological processes such as metabolism, cell signaling, and gene regulation.	EDAM:format_2585
SQLite Format	Data format used by the SQLite embedded relational database engine.	EDAM:format_3621
SVG	Scalable Vector Graphics (SVG), an XML-based vector image format for two-dimensional graphics supporting interactivity and animation.	EDAM:format_3604
Scores Format	Alignment format for score values associated with pairs of sequences.	EDAM:format_1999
Sequence Annotation Track Format	Format of a sequence annotation track, typically displayed as a row of features in a genome browser.	EDAM:format_2919
Sequence Cluster Format	Format used to represent clusters of molecular sequences.	EDAM:format_2170
Sequence Cluster Format (Protein)	Format used to represent clusters of protein sequences.	EDAM:format_2171
Sequence Feature Annotation Format	Data format for molecular sequence feature information.	EDAM:format_1920
Sequence Feature Table Format	Format for a table of sequence features.	EDAM:format_2548
Sequence Feature Table Format (Text)	Text-based format for a table of sequence features.	EDAM:format_2206
Sequence Profile Format	Format of a sequence profile, e.g. summarizing conserved positions across a family of aligned sequences.	EDAM:format_2069
Sequence Range Format	Format used to specify one or more ranges of sequence positions.	EDAM:format_2078
Sequence Record Format	Data format for a molecular sequence record.	EDAM:format_1919
Sequence Trace Format	Format for sequence trace data, including base-call information from a sequencing instrument.	EDAM:format_2057
Sequence Variation Annotation Format	Format of sequence variation annotation, e.g. describing indels, polymorphisms, or structural variants.	EDAM:format_2921
TIFF	Tagged Image File Format (TIFF), a versatile and extensible bitmap image format supporting numerous compression schemes.	EDAM:format_3591
TSV	Tabular data represented as tab-separated values in a text file.	EDAM:format_3475
TXT	Generic plain-text file format, in which data is represented as unstructured or loosely structured human-readable text.	EDAM:format_2330
Tertiary Structure Format	Data format for a molecular tertiary (3D) structure.	EDAM:format_2033
Textual Format	A generic category of formats in which data is represented as plain text.	EDAM:format_2330
Topology Format	Format of topology files containing the static structural information of a molecular system needed for a molecular simulation (e.g. GROMACS TOP, CHARMM PSF, AMBER PRMTOP).	EDAM:format_3879
Trajectory Format	File format used to store trajectory information (e.g. atomic coordinates over time) for a 3D structure, such as from a molecular dynamics simulation.	EDAM:format_3866
VCF	Variant Call Format (VCF), a tabular text format for storing genomic sequence variations such as SNPs, indels, and structural variants.	EDAM:format_3016
Workflow Format	Format used to represent a computational workflow.	EDAM:format_2032
XML	eXtensible Markup Language (XML), a markup format for representing structured, hierarchical data.	EDAM:format_2332
YAML	YAML (YAML Ain't Markup Language), a human-readable, tree-structured data serialization format.	EDAM:format_3750
bedgraph	BedGraph format, a tab-delimited text format for displaying continuous-valued genomic data (e.g. probability scores) as a track.	EDAM:format_3583
bigWig	bigWig format, an indexed binary format for large sequence annotation tracks consisting of a value for each sequence position; similar to the textual WIG format.	EDAM:format_3006
cel	Format of an Affymetrix CEL data file containing (raw) expression intensity information for individual probes on a microarray.	EDAM:format_1638
imzML Metadata File	The metadata XML file (.imzML) component of the imzML mass spectrometry imaging data format, based on mzML, that stores acquisition and instrument metadata; paired with a binary .ibd file containing the mass spectra.	EDAM:format_3682
mzML	mzML, an XML-based format standardized by HUPO PSI for raw mass spectrometer output data; the successor and unifier of the earlier mzData and mzXML formats.	EDAM:format_3244
nii	An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI), commonly used to store brain imaging data obtained via Magnetic Resonance Imaging (MRI).	EDAM:format_3549
pkl	Format used by Python's pickle module for serializing and de-serializing a Python object structure to and from a binary file.	EDAM:format_4002
sif	Simple Interaction Format (SIF), a plain-text network/pathway format used by tools such as Cytoscape to represent nodes and their interactions.	EDAM:format_3619
xls	Microsoft Excel spreadsheet binary file format (.xls), used prior to the introduction of the XML-based .xlsx format.	EDAM:format_3468
xlsx	Microsoft Excel spreadsheet format (.xlsx) consisting of a set of XML documents packaged in a ZIP-compressed container.	EDAM:format_3620
PDB	Protein Data Bank (PDB) format, a text-based format for representing macromolecular tertiary structure (atomic coordinates) and associated metadata, as used by PDB database entries.	EDAM:format_1476
HED	Hierarchical Event Descriptor (HED), a structured vocabulary and format for annotating events in time-series data (e.g. EEG/behavioral data), used within BIDS-formatted neuroimaging datasets.	Not available
MRC	MRC/MRC2014, a binary file format for storing 3D volumetric density map data, widely used in cryo-electron microscopy (cryo-EM) for representing reconstructed density maps.	Not available
Unspecified	Placeholder value used when the specific input/output format for a tool was not specified or is not known.	Not available

Attribute: Tool Output Format

Valid Value	Description	Ontology
Alignment Format	Data format for molecular sequence alignment information.	EDAM:format_1921
Alignment Format (Pair Only)	Data format for molecular sequence alignment information that can hold the alignment of only two sequences.	EDAM:format_2920
Alignment Format (Text)	Text-based format for molecular sequence alignment information.	EDAM:format_2554
Annotated Text Format	Data format of an annotated text, e.g. with recognised entities, concepts, and relations.	EDAM:format_3780
Antimony	A human-readable, text-based modeling language for specifying systems biology models (reaction networks, rate laws, and initial conditions) that can be compiled to SBML; used by tools such as Tellurium/libAntimony.	Not available
BAM	BAM format, the binary, BGZF-compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to a reference sequence; may contain base-call and alignment qualities and other data.	EDAM:format_2572
BCF	The binary version of Variant Call Format (VCF) used to store sequence variation data such as indels, polymorphisms, and structural variants.	EDAM:format_3020
BED	Browser Extensible Data (BED) format for sequence annotation tracks, typically displayed in a genome browser.	EDAM:format_3003
BLAST Results	Format of results from a sequence database search using some variant of BLAST, including score data, alignment data, and summary tables.	EDAM:format_1333
BNGL	BioNetGen Language (BNGL), a format for specifying and simulating rule-based models of biochemical systems such as signal transduction, metabolic, and genetic regulatory networks.	EDAM:format_3972
Binary Format	A generic format in which data is encoded as binary, machine-readable content rather than plain text.	EDAM:format_2333
Biological Model Format	A category of formats used to encode computational or mathematical models of biological systems and processes, such as reaction networks or systems biology models.	EDAM:format_2013
Biological Pathway Or Network Format	Data format for representing a biological pathway or network.	EDAM:format_2013
CSV	Tabular data represented as comma-separated values in a text file.	EDAM:format_3752
Chemical Data Format	Format of a report on a chemical compound or other chemical data.	EDAM:format_2030
Cytoband Format	Format for chromosome cytoband data, reflecting a UCSC Genome Browser database table.	EDAM:format_3235
Cytoscape Input File Format	Format of the Cytoscape input file in which gene expression ratios or values are specified over one or more experiments.	EDAM:format_3477
DCC	A tab-delimited count file produced by the NanoString GeoMx Digital Spatial Profiler, containing per-probe digital count data for a given region of interest.	Not available
DCD	A binary trajectory file format used by molecular dynamics simulation packages such as CHARMM and NAMD to store atomic coordinates (and optionally velocities) over the course of a simulation.	Not available
DSV	Tabular data represented as values delimited by some (non-comma, non-tab) character in a text file.	EDAM:format_3751
Database Hits (Sequence) Format	Format of a report on sequence hits and associated data from searching a sequence database.	EDAM:format_2066
Docker Image Format	A Docker image is a file, comprised of multiple layers, used to execute code in a Docker container; it packages an application together with its dependencies for a complete, executable environment.	EDAM:format_3973
Document Format	Format of documents, including word processor, spreadsheet, and presentation files.	EDAM:format_3507
Dot-Bracket Format	Format for RNA secondary structure using dot-bracket notation, originally generated by the Vienna RNA package/server.	EDAM:format_1457
FASTA	Text-based format for representing nucleotide or peptide sequences, in which each sequence is preceded by a single-line description starting with a '>' character.	EDAM:format_1929
FASTQ	Text-based format for storing both a biological sequence (usually nucleotide) and its corresponding quality scores, most commonly used for raw sequencing reads.	EDAM:format_1930
FASTQ-Illumina	FASTQ short read format variant using the Illumina 1.3+ quality-score encoding scheme.	EDAM:format_1931
FCS	Flow Cytometry Standard (FCS), the standard binary file format for storing multiparameter flow or mass cytometry data produced by cytometry instruments.	OBI:0000327
GCT/Res Format	Tab-delimited text file format (used by GenePattern) containing a column for each sample, a row for each gene, and an expression value for each gene in each sample.	EDAM:format_3709
GFF	General/Generic Feature Format (GFF) for describing genes and other sequence features, of indeterminate version.	EDAM:format_2305
GFF3	Generic Feature Format version 3 (GFF3), a tab-delimited format for describing genomic features with a well-defined hierarchy of parent-child relationships.	EDAM:format_1975
GIF	Graphics Interchange Format, a bitmap image format supporting compression and animation.	EDAM:format_3467
GML	Graph Modeling Language (GML), a plain-text format for describing graph/network data, used by tools such as Cytoscape, Pajek, yEd, and NetworkX.	EDAM:format_3822
GTF	Gene Transfer Format (GTF), a restricted, more strictly-defined version of GFF used to describe gene structure annotations.	EDAM:format_2306
Gene Annotation Format	Format of a report on a particular locus, gene, gene system, or group of genes.	EDAM:format_2031
Gene Cluster Format	A tab-delimited matrix file format that describes a gene expression dataset, where columns correspond to samples/profiles, rows correspond to genes, and cell values correspond to expression measurements.	NCIT:C123891
Gene Expression Report Format	Format of a file of gene expression data, such as a gene expression matrix or profile.	EDAM:format_2058
Genotype And Phenotype Annotation Format	A category of formats used to represent annotations linking genotype data to associated phenotype information, e.g. from studies or databases such as dbGaP.	Not available
Graph Format	Data format for representing graph data, i.e. a set of nodes and the edges connecting them.	EDAM:format_3617
H5AD	HDF5-based binary file format used by the AnnData Python library to store annotated data matrices (e.g. gene expression matrices with associated cell/feature metadata), widely used in single-cell genomics tools such as Scanpy.	Not available
HDF	Hierarchical Data Format (HDF), a set of file formats and libraries for storing and organizing large amounts of numerical data.	EDAM:format_3873
HDF5	HDF5, the current version of the Hierarchical Data Format; a data model, library, and file format for storing and managing large, complex, heterogeneous data.	EDAM:format_3590
HTML	HyperText Markup Language (HTML) format, used for structuring and rendering documents on the web.	EDAM:format_2331
Hidden Markov Model Format	Format for representing a hidden Markov model, e.g. as used for sequence profile searching.	EDAM:format_2072
Image Format	A generic category of formats used for images and associated image metadata.	EDAM:format_3547
Individual Genetic Data Format	Format for metadata describing an individual along with their associated genetic data.	EDAM:format_3287
JPG	Joint Photographic Experts Group (JPEG) format, a common lossy compressed image format.	EDAM:format_3579
JSON	JavaScript Object Notation (JSON), a lightweight, text-based format for representing tree-structured data using key-value pairs.	EDAM:format_3464
LSM	Zeiss' proprietary microscopy image format (based on TIFF), the default data export format for Zeiss LSM-series confocal microscopes, containing image data plus imaging acquisition settings.	EDAM:format_3988
MAF	Mutation Annotation Format (MAF), a tab-delimited text file that aggregates mutation/variant information across a set of samples from one or more VCF files, commonly used in cancer genomics.	NCIT:C172215
MAGE-ML	MAGE-ML, an XML-based format standardized by MGED (now FGED) for representing microarray gene expression data.	EDAM:format_3161
MAGE-TAB	MAGE-TAB, a tab-delimited textual format standardized by MGED (now FGED) for representing microarray gene expression data.	EDAM:format_3162
MAT	A proprietary, binary data container format used by MATLAB software to store workspace variables.	NCIT:C190178
MATLAB Script	File format for scripts or functions written in the MATLAB programming language.	EDAM:format_4007
MSF	A structured (SQLite-based) mass spectrometry result file format used by Thermo Scientific's Proteome Discoverer software.	EDAM:format_3702
Map Format	A format used to encode a genetic or physical map, specifying the positions and/or order of markers such as SNPs or genes along a chromosome (e.g. PLINK MAP files).	EDAM:format_2060
Mass Spectrometry Data Format	Format for mass spectra and derived data, including peptide sequences and related metadata.	EDAM:format_3245
Matrix Format	Format of a matrix (array) of numerical values.	EDAM:format_3033
NIFTI Format	An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI), commonly used to store brain imaging data obtained via Magnetic Resonance Imaging (MRI).	EDAM:format_3549
Nexus Format	Phylogenetic tree Nexus (text) format, used to store aligned sequences and/or tree data along with associated metadata blocks.	EDAM:format_1912
Not Applicable	Placeholder value used when specifying a tool input/output format is not applicable to the entry being described.	Not available
NumPy Format	The standard binary file format used by NumPy - a fundamental Python package for scientific computing - for persisting a single arbitrary NumPy array on disk, including its shape and dtype information.	EDAM:format_4003
OME-TIFF	Open Microscopy Environment TIFF (OME-TIFF), an image file format consisting of standard TIFF/BigTIFF data with OME-XML metadata embedded in the image description, used to store microscopy image data.	EDAM:format_3727
Ontology Format	A generic category of formats used for representing ontologies.	EDAM:format_2195
PDF	Portable Document Format (PDF), a fixed-layout document format for reliably presenting text, images, and formatting independent of application, hardware, or operating system.	EDAM:format_3508
PNG	Portable Network Graphics (PNG), a lossless bitmap image compression format intended to replace GIF.	EDAM:format_3603
PS	PostScript format, a page description language used for representing formatted printable or displayable documents and vector graphics.	EDAM:format_3696
PSF	Protein Structure File (PSF), a structure topology file format used by NAMD and CHARMM molecular simulation programs, containing atoms, bonds, angles, dihedrals, and related force-field terms.	EDAM:format_3882
Phylip Format	PHYLIP format for (aligned) molecular sequences, used by the PHYLIP phylogenetics software package.	EDAM:format_1997
Phylip Format Variant	Some non-standard variant of PHYLIP format for (aligned) sequences.	EDAM:format_2924
Phylogenetic Tree Format	Data format for representing a phylogenetic tree.	EDAM:format_2006
Phylogenetic Tree Format (Text)	Text-based format for representing a phylogenetic tree.	EDAM:format_2556
Protein Interaction Format	Format for molecular (protein-protein) interaction data.	EDAM:format_2054
Python Script	File format for scripts written in Python, a widely used high-level, general-purpose programming language.	EDAM:format_3996
R File Format	File format used for scripts written in the R programming language, executed within the R software environment for statistical computation and graphics.	EDAM:format_3554
R Script	Format for scripts written in the R language, an open-source programming language and environment for statistical computing and graphics.	EDAM:format_3999
RDS	A native binary file format used by R to save and load a single serialized R object to and from a file.	NCIT:C209895
RNA Annotation Format	A general category of formats for annotated RNA data, including e.g. microRNA and RNA-Seq data.	EDAM:format_3865
RNA Secondary Structure Format	Format for the (predicted or experimentally determined) secondary structure of an RNA molecule.	EDAM:format_2076
RPKM	Tab-delimited format for a gene expression levels table, with values calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).	EDAM:format_3980
Raw Sequence Format	Format of a raw molecular sequence, i.e. specifying only the alphabet/characters used with no additional annotation.	EDAM:format_2571
SAM	Sequence Alignment/Map (SAM) format, a text-based format for storing alignments of nucleotide sequences (e.g. sequencing reads) to a reference sequence, including base-call and alignment qualities.	EDAM:format_2573
SBML	Systems Biology Markup Language (SBML), the standard XML format for encoding models of biological processes such as metabolism, cell signaling, and gene regulation.	EDAM:format_2585
SQLite Format	Data format used by the SQLite embedded relational database engine.	EDAM:format_3621
SVG	Scalable Vector Graphics (SVG), an XML-based vector image format for two-dimensional graphics supporting interactivity and animation.	EDAM:format_3604
Scores Format	Alignment format for score values associated with pairs of sequences.	EDAM:format_1999
Sequence Annotation Track Format	Format of a sequence annotation track, typically displayed as a row of features in a genome browser.	EDAM:format_2919
Sequence Cluster Format	Format used to represent clusters of molecular sequences.	EDAM:format_2170
Sequence Cluster Format (Protein)	Format used to represent clusters of protein sequences.	EDAM:format_2171
Sequence Feature Annotation Format	Data format for molecular sequence feature information.	EDAM:format_1920
Sequence Feature Table Format	Format for a table of sequence features.	EDAM:format_2548
Sequence Feature Table Format (Text)	Text-based format for a table of sequence features.	EDAM:format_2206
Sequence Profile Format	Format of a sequence profile, e.g. summarizing conserved positions across a family of aligned sequences.	EDAM:format_2069
Sequence Range Format	Format used to specify one or more ranges of sequence positions.	EDAM:format_2078
Sequence Record Format	Data format for a molecular sequence record.	EDAM:format_1919
Sequence Trace Format	Format for sequence trace data, including base-call information from a sequencing instrument.	EDAM:format_2057
Sequence Variation Annotation Format	Format of sequence variation annotation, e.g. describing indels, polymorphisms, or structural variants.	EDAM:format_2921
TIFF	Tagged Image File Format (TIFF), a versatile and extensible bitmap image format supporting numerous compression schemes.	EDAM:format_3591
TSV	Tabular data represented as tab-separated values in a text file.	EDAM:format_3475
TXT	Generic plain-text file format, in which data is represented as unstructured or loosely structured human-readable text.	EDAM:format_2330
Tertiary Structure Format	Data format for a molecular tertiary (3D) structure.	EDAM:format_2033
Textual Format	A generic category of formats in which data is represented as plain text.	EDAM:format_2330
Topology Format	Format of topology files containing the static structural information of a molecular system needed for a molecular simulation (e.g. GROMACS TOP, CHARMM PSF, AMBER PRMTOP).	EDAM:format_3879
Trajectory Format	File format used to store trajectory information (e.g. atomic coordinates over time) for a 3D structure, such as from a molecular dynamics simulation.	EDAM:format_3866
VCF	Variant Call Format (VCF), a tabular text format for storing genomic sequence variations such as SNPs, indels, and structural variants.	EDAM:format_3016
Workflow Format	Format used to represent a computational workflow.	EDAM:format_2032
XML	eXtensible Markup Language (XML), a markup format for representing structured, hierarchical data.	EDAM:format_2332
YAML	YAML (YAML Ain't Markup Language), a human-readable, tree-structured data serialization format.	EDAM:format_3750
bedgraph	BedGraph format, a tab-delimited text format for displaying continuous-valued genomic data (e.g. probability scores) as a track.	EDAM:format_3583
bigWig	bigWig format, an indexed binary format for large sequence annotation tracks consisting of a value for each sequence position; similar to the textual WIG format.	EDAM:format_3006
cel	Format of an Affymetrix CEL data file containing (raw) expression intensity information for individual probes on a microarray.	EDAM:format_1638
imzML Metadata File	The metadata XML file (.imzML) component of the imzML mass spectrometry imaging data format, based on mzML, that stores acquisition and instrument metadata; paired with a binary .ibd file containing the mass spectra.	EDAM:format_3682
mzML	mzML, an XML-based format standardized by HUPO PSI for raw mass spectrometer output data; the successor and unifier of the earlier mzData and mzXML formats.	EDAM:format_3244
nii	An open file format from the Neuroimaging Informatics Technology Initiative (NIfTI), commonly used to store brain imaging data obtained via Magnetic Resonance Imaging (MRI).	EDAM:format_3549
pkl	Format used by Python's pickle module for serializing and de-serializing a Python object structure to and from a binary file.	EDAM:format_4002
sif	Simple Interaction Format (SIF), a plain-text network/pathway format used by tools such as Cytoscape to represent nodes and their interactions.	EDAM:format_3619
xls	Microsoft Excel spreadsheet binary file format (.xls), used prior to the introduction of the XML-based .xlsx format.	EDAM:format_3468
xlsx	Microsoft Excel spreadsheet format (.xlsx) consisting of a set of XML documents packaged in a ZIP-compressed container.	EDAM:format_3620
PDB	Protein Data Bank (PDB) format, a text-based format for representing macromolecular tertiary structure (atomic coordinates) and associated metadata, as used by PDB database entries.	EDAM:format_1476
HED	Hierarchical Event Descriptor (HED), a structured vocabulary and format for annotating events in time-series data (e.g. EEG/behavioral data), used within BIDS-formatted neuroimaging datasets.	Not available
MRC	MRC/MRC2014, a binary file format for storing 3D volumetric density map data, widely used in cryo-electron microscopy (cryo-EM) for representing reconstructed density maps.	Not available
Unspecified	Placeholder value used when the specific input/output format for a tool was not specified or is not known.	Not available

Attribute: Tool Language

Valid Value	Description	Ontology
AWK	AWK is a text-processing scripting language and command-line utility designed for pattern scanning and manipulation of structured text such as tabular or delimited data.	Not available
ActionScript	ActionScript is an object-oriented programming language originally developed by Macromedia (later Adobe) for building interactive applications and animations on the Adobe Flash Platform.	SWO:0000091
Ada	Ada is a structured, statically typed imperative programming language designed for reliability and maintainability, and widely used in embedded, real-time, and safety-critical systems such as aerospace and defense applications.	SWO:0000092
AppleScript	AppleScript is a scripting language created by Apple that allows users to directly control scriptable Mac applications and automate repetitive tasks on macOS.	SWO:0000093
Assembly Language	Assembly language is a low-level programming language with a close, largely one-to-one correspondence to a computer's machine code instructions, specific to a particular processor architecture.	SWO:0000094
Bash	Bash (Bourne Again SHell) is a Unix shell and command language interpreter widely used as the default login shell and scripting language on Linux and macOS systems.	Not available
C	C is a general-purpose, procedural, statically typed programming language that provides low-level access to memory and hardware, and is widely used for operating systems, embedded systems, and performance-critical software.	SWO:0000095
C#	C# (C Sharp) is a general-purpose, object-oriented programming language developed by Microsoft as part of the .NET platform, commonly used for Windows applications, games, and web services.	SWO:0000096
C++	C++ is a general-purpose, statically typed programming language that extends the C language with object-oriented and generic programming features, widely used for systems software, games, and performance-critical applications.	SWO:0000097
COBOL	COBOL (Common Business-Oriented Language) is an imperative, procedural programming language designed for business, finance, and administrative data-processing applications.	SWO:0000098
CSS	CSS (Cascading Style Sheets) is a style sheet language used to describe the presentation and formatting of documents written in HTML or XML.	Not available
CWL	Common Workflow Language (CWL) is a specification for describing command-line tools and workflows for data-intensive scientific analysis in a portable and scalable way.	EDAM:format_3857
ColdFusion	ColdFusion is a commercial rapid-application-development scripting language and platform, originally created by Allaire, used for building dynamic web applications.	SWO:0000099
D	D is a general-purpose, statically typed systems programming language that combines the efficiency of C++ with modern features such as garbage collection and built-in unit testing.	SWO:0000100
Delphi	Delphi is an integrated development environment and associated Object Pascal-based programming language used primarily for rapid application development of Windows desktop and mobile applications.	SWO:0000101
Dockerfile	A Dockerfile is a text document containing a series of instructions used to automatically build a Docker container image.	Not available
Dylan	Dylan is a multi-paradigm programming language that combines features of dynamic, object-oriented languages such as Lisp and Smalltalk with a more conventional syntax.	SWO:0000102
Eiffel	Eiffel is an object-oriented programming language designed around the principle of Design by Contract, emphasizing software correctness and reliability.	SWO:0000103
Elm	Elm is a functional programming language that compiles to JavaScript, designed for building reliable web applications with a strong emphasis on usability and type safety.	Not available
Forth	Forth is a stack-based, procedural programming language known for its simplicity, extensibility, and use of Reverse Polish Notation, historically popular for embedded and control systems.	SWO:0000104
Fortran	Fortran (Formula Translation) is a general-purpose, imperative programming language especially suited for numeric computation and scientific computing.	SWO:0000105
Go	Go (Golang) is a statically typed, compiled programming language developed by Google, designed for simplicity, concurrency, and efficiency in building scalable software and networked services.	Not available
Groovy	Groovy is a dynamic, object-oriented programming language for the Java platform that adds scripting capabilities and syntactic sugar to Java-based applications.	SWO:0000106
HTML	HTML (Hypertext Markup Language) is a standard markup language used to structure and display content on web pages, as specified by the World Wide Web Consortium (W3C).	NCIT:C142380
Haskell	Haskell is a statically typed, purely functional programming language known for its strong emphasis on lazy evaluation and mathematical rigor.	SWO:0000107
Icarus	Icarus Verilog is an open-source compiler and simulator for the Verilog hardware description language, used for digital circuit design and simulation.	Not available
JSP	JavaServer Pages (JSP) is a Java-based technology that enables embedding Java code and dynamic content directly within HTML web pages for server-side rendering.	Not available
Java	Java is a general-purpose, class-based, object-oriented programming language designed to be portable across platforms via the 'write once, run anywhere' principle, executed on the Java Virtual Machine.	SWO:0000012
JavaScript	JavaScript is a high-level, dynamically typed scripting language most commonly used to add interactivity and dynamic behavior to web pages, and increasingly for server-side and application development.	SWO:0000108
Julia	Julia is a high-level, high-performance dynamic programming language designed for numerical and scientific computing, combining ease of use with speed comparable to statically typed languages.	Not available
LabVIEW	LabVIEW is a graphical, dataflow-based programming environment developed by National Instruments, primarily used for data acquisition, instrument control, and industrial automation.	SWO:0000109
Lisp	Lisp is a family of programming languages characterized by a distinctive fully parenthesized syntax and support for symbolic computation, historically influential in artificial intelligence research.	SWO:0000110
Lua	Lua is a lightweight, high-level, embeddable scripting language designed for extensibility, commonly used to add scripting capabilities to applications and games.	SWO:0000111
MATLAB	MATLAB is a high-level language and interactive environment that enables users to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.	SWO:0000005
MLXTRAN	MLXTRAN is a domain-specific modeling language used within the Monolix software suite to define pharmacometric and biological models for nonlinear mixed-effects analysis.	SWO:0000134
Maple	Maple is a symbolic and numeric computing environment and programming language used for mathematical computation, modeling, and visualization.	SWO:0000112
Mathematica	Mathematica is a computational software system and programming language developed by Wolfram Research, used for symbolic and numerical computation, data analysis, and visualization.	SWO:0000113
NMTRAN	NM-TRAN is the control-file language used by the NONMEM software package to specify nonlinear mixed-effects pharmacokinetic/pharmacodynamic models.	SWO:0000136
Netlogo	NetLogo is a multi-agent programmable modeling environment used for simulating and exploring complex natural and social phenomena.	Not available
Nextflow	Nextflow is a workflow system for creating scalable, portable, and reproducible data analysis pipelines.	EDAM:format_4048
Ocaml	OCaml is a general-purpose, statically typed functional programming language that also supports imperative and object-oriented programming styles.	Not available
OpenEdge ABL	OpenEdge ABL (Advanced Business Language) is a proprietary fourth-generation programming language developed by Progress Software for building business applications.	Not available
Other	A programming or software language used by a tool that is not otherwise represented among the listed valid values.	Not available
PHP	PHP is a general-purpose scripting language especially suited for server-side web development, used to create dynamic web pages and applications.	SWO:0000116
Pascal	Pascal is a procedural, statically typed imperative programming language designed to encourage structured programming practices, historically widely used for teaching and application development.	SWO:0000114
Perl	Perl is a high-level, general-purpose interpreted programming language known for its powerful text-processing capabilities, widely used for system administration, web development, and bioinformatics.	SWO:0000115
PostScript	PostScript is a page description and programming language developed by Adobe, used primarily for describing the layout, text, and graphics of printed documents.	SWO:3000024
PowerShell	PowerShell is a task automation and configuration management framework from Microsoft, consisting of a command-line shell and an associated scripting language built on .NET.	Not available
Prolog	Prolog is a logic programming language based on formal logic, in which programs are expressed as facts and rules, widely used in artificial intelligence and computational linguistics.	SWO:0000117
PyMOL	PyMOL is a molecular visualization and modeling software system with an embedded Python-based scripting interface, widely used for rendering and analyzing 3D structures of proteins and other molecules.	Not available
Python	Python is a widely used general-purpose, high-level programming language whose design philosophy emphasizes code readability, supporting object-oriented, imperative, and functional programming styles.	SWO:0000118
R	R is a programming language and free software environment for statistical computing, data analysis, and graphics, widely used in bioinformatics and data science.	SWO:0000415
REXX	REXX (Restructured Extended Executor) is a structured, interpreted programming language originally developed by IBM for scripting and automating tasks on mainframe systems.	SWO:0000119
Racket	Racket is a general-purpose, multi-paradigm programming language descended from Scheme, used both as a teaching language and for general software development.	SWO:0000008
Ruby	Ruby is a dynamic, object-oriented, general-purpose programming language designed for simplicity and productivity, with an elegant and readable syntax.	SWO:0000120
SAS	SAS is a proprietary software suite and programming language developed by SAS Institute for advanced analytics, statistical analysis, business intelligence, and data management.	SWO:0000121
SQL	SQL (Structured Query Language) is an industry-standard language for creating, updating, and querying relational database management systems.	NCIT:C54108
Scala	Scala is a general-purpose programming language that combines object-oriented and functional programming paradigms, and runs on the Java Virtual Machine.	SWO:0000122
Scheme	Scheme is a minimalist, multi-paradigm programming language and dialect of Lisp known for its simple syntax and support for functional programming.	SWO:0000123
Shell	Shell refers to a command-line interpreter and associated scripting language used to execute commands and automate tasks in Unix-like operating systems.	SWO:0000124
TeX	TeX is a typesetting system and programming language created by Donald Knuth, widely used for producing technical and scientific documents with precise typographic control.	Not available
Turing	Turing is a structured, general-purpose programming language developed at the University of Toronto, designed primarily for teaching programming concepts.	SWO:0000127
VHDL	VHDL (VHSIC Hardware Description Language) is a hardware description language used to model and simulate the behavior and structure of digital electronic circuits.	SWO:0000129
Verilog	Verilog is a hardware description language used to model, design, and simulate digital and analog electronic systems.	SWO:0000128
Visual Basic	Visual Basic is an event-driven, object-oriented programming language developed by Microsoft, historically used for rapid application development of Windows desktop applications.	SWO:0000130
WDL	WDL (Workflow Description Language) is a human-readable and writable language for specifying data processing workflows, commonly used in bioinformatics pipelines.	Not available
XAML	XAML (Extensible Application Markup Language) is a declarative XML-based markup language used to define user interfaces and object hierarchies in Microsoft applications such as WPF and UWP.	Not available

Attribute: Tool Link Type

Valid Value	Description	Ontology
Discussion Forum	A link to an online forum or discussion board for the tool.	GSSO:005459
Galaxy Service	A link to an instance of the tool hosted as a Galaxy service.	Not available
Helpdesk	A phone line, web site or email-based system providing help to the end-user of the software.	Not available
Issue Tracker	A link to the tool's issue tracker for reporting bugs or requesting features.	Not available
Mailing list	Mailing list for the software announcements, discussions, support etc.	Not available
Mirror	Mirror of an (identical) online service.	Not available
Other	Other type of link for software - the default if a more specific type is not available.	Not available
Repository	A place where source code, data and other files can be retrieved from, typically via platforms like GitHub which provide version control and other features, or something simpler, e.g. an FTP site.	APOLLO_SV:00000522
Service	An online service (other than Galaxy) that provides access (an interface) to the software.	NCIT:C80736
Social Media	A link to a social media account associated with the tool.	MESH:D061108
Software Catalogue	A link to an entry for the tool in a software catalogue or registry.	Not available
Technical Monitoring	A link to a status/monitoring page reporting the tool's operational availability.	Not available

Attribute: Tool Operating System

Valid Value	Description	Ontology
Linux	All flavours of Linux/UNIX operating systems.	SWO:0000022
Mac	All flavours of Apple Macintosh operating systems (primarily Mac OS X).	SWO:0000151
Windows	All flavours of Microsoft Windows operating system.	SWO:9000072

Attribute: Tool Operation

Valid Value	Description	Ontology
Aggregation	Combine multiple files or data items into a single file or object.	EDAM:operation_3436
Allele Frequency Distribution Analysis	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).	EDAM:operation_0554
Analysis	Apply analytical methods to existing data of a specific type.	EDAM:operation_2945
Annotation	Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary.	EDAM:operation_0226
Box-Whisker Plot Plotting	Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles.	EDAM:operation_2943
Calculation	Mathematical determination of the value of something, typically a properly of a molecule.	EDAM:operation_3438
Cell Migration Analysis	Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression.	EDAM:operation_3446
Cell Modelling	No description provided	Not available
Cell Number Quantification	No description provided	Not available
Cell Type Enrichment Analysis	No description provided	Not available
Classification	Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category.	EDAM:operation_2990
Clustering	Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters).	EDAM:operation_3432
Clustering Profile Plotting	Visualise clustered quantitative data as set of different profiles, where each profile is plotted versus different entities or samples on the X-axis.	EDAM:operation_2935
Comparison	Compare two or more things to identify similarities.	EDAM:operation_2424
Conversion	Convert a data set from one form to another.	EDAM:operation_3434
Copy Number Variation Detection	Identify where sections of the genome are repeated and the number of repeats in the genome varies between individuals.	EDAM:operation_3961
Correlation	Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data.	EDAM:operation_3465
DNA Barcoding	Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms.	EDAM:operation_3200
Data Handling	Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output.	EDAM:operation_2409
Data Retrieval	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...	EDAM:operation_2422
Database Search	Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query.	EDAM:operation_2421
De Novo Sequencing	Analytical process that derives a peptide's amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database.	EDAM:operation_3644
Demultiplexing	Assigning sequence reads to separate groups / files based on their index tag (sample origin).	EDAM:operation_3933
Differential Gene Expression Profiling	Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.	EDAM:operation_3223
Differential Protein Expression Profiling	The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup.	EDAM:operation_3741
Dimensionality Reduction	A process used in statistics, machine learning, and information theory that reduces the number of random variables by obtaining a set of principal variables.	EDAM:operation_3935
Editing	Edit a data entity, either randomly or specifically.	EDAM:operation_3096
Enrichment Analysis	Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed.	EDAM:operation_3501
Expression Analysis	Process (read and/or write) expression data from experiments measuring molecules (e.g. omics data), including analysis of one or more expression profiles, typically to interpret them in functional terms.	EDAM:operation_2495
Expression Correlation Analysis	Analyse the correlation patterns among features/molecules across across a variety of experiments, samples etc.	EDAM:operation_3463
Expression Data Visualisation	Visualise microarray or other expression data.	EDAM:operation_0571
Expression Profile Clustering	Perform cluster analysis of expression data to identify groups with similar expression profiles, for example by clustering.	EDAM:operation_0313
Expression Profile Comparison	Comparison of expression profiles.	EDAM:operation_0315
Functional Clustering	Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype.	EDAM:operation_3459
Gene Expression Profiling	The measurement of the activity (expression) of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function.	EDAM:operation_0314
Gene Methylation Analysis	Analysing the DNA methylation of specific genes or regions of interest.	EDAM:operation_3207
Gene Regulatory Network Analysis	Analyse a known network of gene regulation.	EDAM:operation_1781
Gene Regulatory Network Prediction	Predict a network of gene regulation.	EDAM:operation_2437
Gene-Set Enrichment Analysis	Identify classes of genes or proteins that are over or under-represented in a large set of genes or proteins. For example analysis of a set of genes corresponding to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO...	EDAM:operation_2436
Generation	Construct some data entity.	EDAM:operation_3429
Genetic Mapping	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.	EDAM:operation_0282
Genetic Variation Analysis	Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.	EDAM:operation_3197
Genome Analysis	Study of genomic feature structure, variation, function and evolution at a genomic scale.	EDAM:operation_3918
Genome Annotation	Annotate a genome sequence with terms from a controlled vocabulary.	EDAM:operation_0362
Genome Visualisation	Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence.	EDAM:operation_3208
Genotyping	Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.	EDAM:operation_3196
Heat Map Generation	Generate a heat map of expression data from e.g. microarray data.	EDAM:operation_0531
Image Analysis	The analysis of a image (typically a digital image) of some type in order to extract information from it.	EDAM:operation_3443
Imputation	Replace missing data with substituted values, usually by using some statistical or other mathematical approach.	EDAM:operation_3557
Incident Curve Plotting	Plot an incident curve such as a survival curve, death curve, mortality curve.	EDAM:operation_3503
Information Retrieval	Retrieve resources from information systems matching a specific information need.	EDAM:operation_3908
Linkage Analysis	Analyse genetic linkage.	EDAM:operation_0283
Mapping	Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.	EDAM:operation_2429
Metabolic Pathway Prediction	Predict a metabolic pathway.	EDAM:operation_3929
Methylation Analysis	Analyse cytosine methylation states in nucleic acid sequences.	EDAM:operation_3204
Microscope Image Visualisation	Visualise images resulting from various types of microscopy.	EDAM:operation_3552
Modelling and Simulation	Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.	EDAM:operation_2426
Molecular Dynamics	The simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.	EDAM:operation_2476
Network Analysis	Generate, process or analyse a biological network.	EDAM:operation_3927
Network Visualisation	Render (visualise) a network - typically a biological network of some sort.	EDAM:operation_3925
Nucleic Acid Feature Detection	Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.	EDAM:operation_0415
Nucleic Acid Sequence Analysis	Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences).	EDAM:operation_2478
Nucleosome Position Prediction	Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA.	EDAM:operation_0432
Ontology Visualisation	Visualise, format or render data from an ontology, typically a tree of terms.	EDAM:operation_3559
Pathway Analysis	Generate, process or analyse a biological pathway.	EDAM:operation_3928
Pathway Modelling	Model a metabolic network. This can include 1) reconstruction to break down a metabolic pathways into reactions, enzymes, and other relevant information, and compilation of this into a mathematical model and 2) simulations of metabolism based on the model.	EDAM:operation_3660
Peak Calling	Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.	EDAM:operation_3222
Phylogenetic Analysis	Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions.	EDAM:operation_0324
Prediction and Recognition	Predict, recognise, detect or identify some properties of a biomolecule.	EDAM:operation_2423
Principal Component Analysis	A statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components.	EDAM:operation_3960
Protein Comparison	Compare two or more proteins (or some aspect) to identify similarities.	EDAM:operation_2997
Protein Function Comparison	Compare the functional properties of two or more proteins.	EDAM:operation_1778
Protein Function Prediction	Predict the biological or biochemical role of a protein, or other aspects of a protein function.	EDAM:operation_1777
Protein Identification	Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry.	EDAM:operation_3767
Protein Interaction Network Analysis	Analyse a network of protein interactions.	EDAM:operation_0276
Protein Quantification	Technique for determining the amount of proteins in a sample.	EDAM:operation_3630
Protein-Protein Interaction Analysis	Analyse the interactions of proteins with other proteins.	EDAM:operation_2949
Quantification	Counting and measuring experimentally determined observations into quantities.	EDAM:operation_3799
Query and Retrieval	Search or query a data resource and retrieve entries and / or annotation.	EDAM:operation_0224
RNA Secondary Structure Prediction	Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc).	EDAM:operation_0278
RNA-Seq Analysis	Analyze data from RNA-seq experiments.	EDAM:operation_3680
RNA-Seq Quantification	Quantification of data arising from RNA-Seq high-throughput sequencing, typically the quantification of transcript abundances durnig transcriptome analysis in a gene expression study.	EDAM:operation_3800
Regression Analysis	A statistical calculation to estimate the relationships among variables.	EDAM:operation_3659
SNP Annotation	Predict the effect or function of an individual single nucleotide polymorphism (SNP).	EDAM:operation_3661
SNP Detection	Find single nucleotide polymorphisms (SNPs) - single nucleotide change in base positions - between sequences. Typically done for sequences from a high-throughput sequencing experiment that differ from a reference genome and which might, especially by reference to population frequency or functional...	EDAM:operation_0484
Scatter Plot Plotting	Render a graph in which the values of two variables are plotted along two axes; the pattern of the points reveals any correlation.	EDAM:operation_2940
Sequence Alignment Analysis	Analyse a molecular sequence alignment.	EDAM:operation_0258
Sequence Alignment Comparison	Compare (typically by aligning) two molecular sequence alignments.	EDAM:operation_0259
Sequence Analysis	Analyse one or more known molecular sequences.	EDAM:operation_2403
Sequence Annotation	Annotate a molecular sequence record with terms from a controlled vocabulary.	EDAM:operation_0361
Sequence Classification	Assign molecular sequence(s) to a group or category.	EDAM:operation_2995
Sequence Cluster Visualisation	Visualise, format or render sequence clusters.	EDAM:operation_0566
Sequence Clustering	Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences.	EDAM:operation_0291
Sequence Comparison	Compare two or more molecular sequences.	EDAM:operation_2451
Sequence Composition Calculation	Calculate character or word composition or frequency of a molecular sequence.	EDAM:operation_0236
Sequence Editing	Edit or change a molecular sequence, either randomly or specifically.	EDAM:operation_0231
Sequence File Editing	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, creation of subset or a new file of sequences.	EDAM:operation_2121
Sequence Read Processing	The processing of reads from high-throughput sequencing machines.	EDAM:operation_3921
Sequencing Quality Control	Raw sequence data quality control.	EDAM:operation_3218
Simulated Gene Expression Data Generation	Simulate gene expression data, e.g. for purposes of benchmarking.	EDAM:operation_3566
Sorting	Sort a set of files or data items according to some property.	EDAM:operation_3802
Spectral Analysis	Analyse one or more spectra from mass spectrometry (or other) experiments.	EDAM:operation_3214
Standardisation and Normalisation	Standardize or normalize data by some statistical method.	EDAM:operation_3435
Statistical Calculation	Perform a statistical data operation of some type, e.g. calibration or validation.	EDAM:operation_2238
Statistical Inference	Analyse data in order to deduce properties of an underlying distribution or population.	EDAM:operation_3658
Statistical Modelling	Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data.	EDAM:operation_3664
Structural Variation Detection	Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).	EDAM:operation_3228
Structure Analysis	Analyse known molecular tertiary structures.	EDAM:operation_2480
Text Mining	Process and analyse text (typically scientific literature) to extract information from it.	EDAM:operation_0306
Tissue Modelling	Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models.	EDAM:operation_2426
Validation	Validate some data.	EDAM:operation_2428
Variant Calling	Detect, identify and map mutations, such as single nucleotide polymorphisms, short indels and structural variants, in multiple DNA sequences. Typically the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware, to study genomic alterations.	EDAM:operation_3227
Variant Classification	Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins.	EDAM:operation_3225
Variant Effect Prediction	Predict the effect of point mutation on a protein structure, in terms of structural effects and protein folding, stability and function.	EDAM:operation_0331
Visualisation	Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures.	EDAM:operation_0337
scRNA-Seq Analysis	Analyze data from RNA-seq experiments.	EDAM:operation_3680
Agent-Based Cell Modelling	Synonym: multi-agent model	MAMO:0000024
Not Applicable	No description provided	Not available

Attribute: Tool Topic

Valid Value	Description	Ontology
Allergy Clinical Immunology and Immunotherapeutics	Health issues related to the immune system and their prevention, diagnosis and management.	EDAM:topic_3400
Biochemistry	Chemical substances and physico-chemical processes and that occur within living organisms.	EDAM:topic_3292
Bioimaging	The use of imaging techniques to understand biology.	EDAM:topic_3383
Bioinformatics	The archival, curation, processing and analysis of complex biological data.	EDAM:topic_0091
Biological Databases	The general handling of data stored in digital archives such as databases, databanks, web portals, and other data resources.	EDAM:topic_3489
Biology	The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on.	EDAM:topic_3070
Biomedical Science	Topic concerning biological science that is (typically) performed in the context of medicine.	EDAM:topic_3344
Biomolecular Simulation	The study and simulation of molecular conformations using a computational model and computer simulations.	EDAM:topic_3892
Biophysics	The use of physics to study biological system.	EDAM:topic_3306
Biotechnology	The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production.	EDAM:topic_3297
Biotherapeutics	The process of formulating and administering a pharmaceutical compound to achieve a therapeutic effect.	EDAM:topic_3374
Cell Biology	Cells, such as key genes and proteins involved in the cell cycle.	EDAM:topic_2229
Cell Culture Collection	Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells.	EDAM:topic_3340
Chemistry	The composition and properties of matter, reactions, and the use of reactions to create new substances.	EDAM:topic_3314
Chip-Seq	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.	EDAM:topic_3169
Chromosome Conformation Capture	Molecular biology methods used to analyze the spatial organization of chromatin in a cell.	EDAM:topic_3940
Comparative Genomics	The study (typically comparison) of the sequence, structure or function of multiple genomes.	EDAM:topic_0797
Compound Libraries and Screening	Collections of chemicals, typically for use in high-throughput screening experiments.	EDAM:topic_3343
Computational Biology	The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.	EDAM:topic_3307
Computer Science	The theory and practical use of computer systems.	EDAM:topic_3316
Cytogenetics	The branch of genetics concerned with the relationships between chromosomes and cellular behaviour, especially during mitosis and meiosis.	EDAM:topic_3959
Cytometry	Cytometry is the measurement of the characteristics of cells.	EDAM:topic_3934
DNA	DNA sequences and structure, including processes such as methylation and replication.	EDAM:topic_0654
DNA Mutation	DNA mutation.	EDAM:topic_2533
DNA Packaging	DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures.	EDAM:topic_3176
DNA Polymorphism	DNA polymorphism.	EDAM:topic_2885
Data Architecture Analysis and Design	The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.	EDAM:topic_3365
Data Identity and Mapping	Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases.	EDAM:topic_3345
Data Mining	The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format.	EDAM:topic_3473
Data Submission Annotation and Curation	Data curation and archival includes the preservation of data in a repository, archive, or a deposition database; and curation of data and metadata, database accessions, annotation, and data provenance.	EDAM:topic_0219
Data Visualisation	Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data.	EDAM:topic_0092
Developmental Biology	How organisms grow and develop.	EDAM:topic_3064
Drug Development	The process of bringing a new drug to market once a lead compounds has been identified through drug discovery.	EDAM:topic_3373
Drug Discovery	The discovery and design of drugs or potential drug compounds.	EDAM:topic_3336
Drug Metabolism	The study of how a drug interacts with the body.	EDAM:topic_3375
Electron Microscopy	The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.	EDAM:topic_0611
Epigenetics	Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.	EDAM:topic_3295
Evolutionary Biology	The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity.	EDAM:topic_3299
Exome Sequencing	Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome.	EDAM:topic_3676
Experimental Design and Studies	The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions.	EDAM:topic_3678
Function Analysis	The study of gene and protein function including the prediction of functional properties of a protein.	EDAM:topic_1775
Functional Genomics	The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc.	EDAM:topic_0085
Functional Regulatory and Non-Coding RNA	Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).	EDAM:topic_0659
GWAS Study	Genome-wide association study experiments.	EDAM:topic_3517
Gene Expression	The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.	EDAM:topic_0203
Gene Regulation	The regulation of gene expression.	EDAM:topic_0204
Gene Structure	Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.	EDAM:topic_0114
Gene Transcripts	Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.	EDAM:topic_3512
Gene and Protein Families	Particular gene(s), gene family or other gene group or system and their encoded proteins.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...	EDAM:topic_0623
Genetic Engineering	The application of biotechnology to directly manipulate an organism's genes.	EDAM:topic_3912
Genetic Variation	Stable, naturally occurring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms.	EDAM:topic_0199
Genetics	The study of genes, genetic variation and heredity in living organisms.	EDAM:topic_3053
Genomics	Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.	EDAM:topic_0622
Genotype and Phenotype	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,...	EDAM:topic_0625
Imaging	The visual representation of an object.	EDAM:topic_3382
Immunoinformatics	Immunoinformatics is the field of computational biology that deals with the study of immunoloogical questions. Immunoinformatics is at the interface between immunology and computer science. It takes advantage of computational, statistical, mathematical approaches and enhances the understanding of...	EDAM:topic_3948
Immunology	The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on.	EDAM:topic_0804
Immunomics	The study of immune system as a whole, its regulation and response to pathogens using genome-wide approaches.	EDAM:topic_3967
Immunoprecipitation Experiment	Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq.	EDAM:topic_3656
Immunoproteins and Antigens	Immunity-related proteins and their ligands.	EDAM:topic_2830
Infectious Disease	The branch of medicine that deals with the prevention, diagnosis and management of transmissible disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions).	EDAM:topic_3324
Informatics	The study and practice of information processing and use of computer information systems.	EDAM:topic_0605
Laboratory Techniques	No description provided	Not available
Light Microscopy	The use of optical instruments to magnify the image of an object.	EDAM:topic_3385
Lipids	Lipids and their structures.	EDAM:topic_0153
Machine Learning	A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an output, rather than relying on explicitly encoded information only.	EDAM:topic_3474
Mapping	The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS...	EDAM:topic_0102
Mathematics	The study of numbers (quantity) and other topics including structure, space, and change.	EDAM:topic_3315
Medical Imaging	The use of imaging techniques for clinical purposes for medical research.	EDAM:topic_3384
Medical Informatics	The application of information technology to health, disease and biomedicine.	EDAM:topic_3063
Medicine	Research in support of healing by diagnosis, treatment, and prevention of disease.	EDAM:topic_3303
Medicines Research and Development	The discovery, development and approval of medicines.	EDAM:topic_3376
Membrane and Lipoproteins	Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane.	EDAM:topic_0820
Metagenomics	The study of genetic material recovered from environmental samples, and associated environmental data.	EDAM:topic_3174
Molecular Biology	The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life.	EDAM:topic_3047
Molecular Genetics	The structure and function of genes at a molecular level.	EDAM:topic_3321
Molecular Interactions Pathways and Networks	Molecular interactions, biological pathways, networks and other models.	EDAM:topic_0602
Nucleic Acid Structure Analysis	The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.	EDAM:topic_0097
Nucleic Acids	The processing and analysis of nucleic acid sequence, structural and other data.	EDAM:topic_0077
Omics	The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.	EDAM:topic_3391
Oncology	The study of cancer, for example, genes and proteins implicated in cancer.	EDAM:topic_2640
Ontology and Terminology	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.	EDAM:topic_0089
Pathology	Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases.	EDAM:topic_0634
Pharmacogenomics	The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.	EDAM:topic_0208
Pharmacology	The study of drugs and their effects or responses in living systems.	EDAM:topic_0202
Pharmacovigilance	The detection, assessment, understanding and prevention of adverse effects of medicines.	EDAM:topic_3378
Phylogenetics	The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences).	EDAM:topic_3293
Phylogenomics	The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction.	EDAM:topic_0194
Phylogeny	The study of evolutionary relationships amongst organisms.	EDAM:topic_0084
Preclinical and Clinical Studies	The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities.	EDAM:topic_3379
Probes and Primers	Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence.	EDAM:topic_0632
Protein Expression	The translation of mRNA into protein and subsequent protein processing in the cell.	EDAM:topic_0108
Protein Modifications	Protein chemical modifications, e.g. post-translational modifications.	EDAM:topic_0601
Protein Properties	The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein.	EDAM:topic_0123
Proteins	Archival, processing and analysis of protein data, typically molecular sequence and structural data.	EDAM:topic_0078
Proteomics	Proteomics is in the narrow sense (sensu stricto) the application of methods to separate, characterise, identify, and quantify all proteins (the proteome) - or a substantial set of proteins - that are present in a sample. Proteomics in the broad sense is the science of proteins and peptides on the...	EDAM:topic_0121
Proteomics Experiment	Proteomics experiments.	EDAM:topic_3520
RNA	RNA sequences and structures.	EDAM:topic_0099
RNA-Seq	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.	EDAM:topic_3170
Safety Sciences	The safety (or lack) of drugs and other medical interventions.	EDAM:topic_3377
Sample Collections	Biological samples and specimens.	EDAM:topic_3277
Sequence Analysis	The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles.	EDAM:topic_0080
Sequencing	The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.	EDAM:topic_3168
Simulation Experiment	Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction.	EDAM:topic_3524
Software Engineering	The process that leads from an original formulation of a computing problem to executable programs.	EDAM:topic_3372
Statistics and Probability	The application of statistical methods to biological problems.	EDAM:topic_2269
Structural Analysis	The curation, processing, analysis and prediction of data about the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.	EDAM:topic_0081
Structural Biology	The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.	EDAM:topic_1317
Systems Biology	The holistic modelling and analysis of complex biological systems and the interactions therein.	EDAM:topic_2259
Transcription Factors and Regulatory Sites	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.	EDAM:topic_0749
Transcriptomics	The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc.	EDAM:topic_3308
Virology	Study of viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation.	EDAM:topic_0781
Whole Genome Sequencing	Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time.	EDAM:topic_3673
Workflows	Biological or biomedical analytical workflows or pipelines.	EDAM:topic_0769
scRNA-Seq	Combined with NGS (Next Generation Sequencing) technologies, single-cell sequencing allows the study of genetic information (DNA, RNA, epigenome...) at a single cell level. It is often used for differential analysis and gene expression profiling.	EDAM:topic_4028

Attribute: Tool Type

Valid Value	Description	Ontology
Bioinformatics Portal	A web-based portal providing access to bioinformatics data, tools, or analyses.	Not available
Command-Line Tool	A tool operated via a command-line interface.	SWO:0000030
Database Portal	A web-based portal providing access to a structured database.	Not available
Desktop Application	A standalone application installed and run locally on a user's computer.	Not available
Library	A collection of components that are used to construct other tools. bio.tools scope includes component libraries performing high-level bioinformatics functions but excludes lower-level programming libraries.	IAO:0000593
Notebook	An interactive computational notebook (e.g., Jupyter/R Markdown) combining code, output, and narrative text.	Not available
Ontology	A collection of information about concepts, including terms, synonyms, descriptions etc.	EDAM:data_0582
Other	A tool type not covered by any of the other listed values.	Not available
Plug-In	A software component that adds functionality to an existing application or platform.	SWO:0000083
SPARQL Endpoint	A web service that accepts SPARQL queries against an RDF data store.	EDAM:format_3790
Script	A tool written for some run-time environment (e.g. other applications or an OS shell) that automates the execution of tasks. Often a small program written in a general-purpose languages (e.g. Perl, Python) or some domain-specific languages (e.g. sed).	NCIT:C96999
Serialized Model	A pre-trained or pre-built computational model distributed in a serialized/saved format.	Not available
Suite	A collection of tools which are bundled together into a convenient toolkit. Such tools typically share related functionality, a common user interface and can exchange data conveniently. This includes collections of stand-alone command-line tools, or Web applications within a common portal.	Not available
Web API	An application programming interface (API) consisting of endpoints to a request-response message system accessible via HTTP. Includes everything from simple data-access URLs to RESTful APIs.	NCIT:C75301
Web Application	A tool accessed and operated through a web browser.	NCIT:C172305
Web Service	A tool that exposes its functionality over the web via an API, typically consumed programmatically rather than through a user interface.	NCIT:C45412
Workbench	An application or suite with a graphical user interface, providing an integrated environment for data analysis which includes or may be extended with any number of functions or tools. Includes workflow systems, platforms, frameworks etc.	Not available
Workflow	A set of tools which have been composed together into a pipeline of some sort. Such tools are (typically) standalone, but are composed for convenience, for instance for batch execution via some workflow engine or script.	NCIT:C42753

Attribute: Tool Package Dependencies Present

Valid Value	Description	Ontology
True	Conforming to facts, reality, or definitive criteria.	NCIT:C68850
False	Not in accordance with facts, reality, or definitive criteria.	NCIT:C68851

Attribute: Tool Entity Role

Valid Value	Description	Ontology
Developer	An individual or organization responsible for writing and maintaining the software's source code.	credit:software
Maintainer	An individual or organization responsible for managing updates, fixes, and ongoing upkeep of the software.	schema:maintainer
Provider	A role which inheres in a person or organization and is realized in a planned process which provides access to training, materials or execution of protocols for an organization or person.	OBI:0000947
Documentor	A documentation role that involves preparation of instruction manuals, journal articles, and other supporting documents to communicate complex and technical information more easily.	CRO:0000091
Contributor	An individual or organization that has made a contribution to the resource, distinct from its primary developer(s).	DCTERMS:contributor
Support	No description provided	Not available
Primary Contact	The main or principle contact person for a study.	NCIT:C127533

Attribute: Tool Entity Type

Valid Value	Description	Ontology
Person	A human being.	NCIT:C25190
Project	Any specifically defined piece of work that is undertaken or attempted to meet a single requirement.	NCIT:C47885
Division	An administrative unit within a government, academic organization or business.	NCIT:C85531
Institute	An organization founded for the promotion of scientific research or education.	SIO:000688
Research Consortium	Groups of scientists who link their expertise and resources in collaborative efforts to address important questions of shared interest.	NCIT:C19975
Funding Agency	An organization that underwrites financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.	NCIT:C39409