Keywords and Expertise

One or more molecular sequences, possibly with associated annotation.|This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.

Data (typically biological or biomedical) that has been rendered into an image, typically for display on screen.

Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.

Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.

A map of (typically one) DNA sequence annotated with positional or non-positional features.

An array of numerical values.|This is a broad data type and is used a placeholder for other, more specific types.

An alignment of molecular sequences, structures or profiles derived from them.

Annotation on a biological sample, for example experimental factors and their values.|This might include compound and dose in a dose response experiment.

A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol.

Name or other identifier of an entry from a biosample database.

An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database.

Raw sequence reads refer to the unprocessed data generated by DNA sequencing technology, which contains the nucleotide information of the genome of interest. In bacterial genomics, raw sequence reads are used to assemble the genomic sequence of the bacteria and to identify genetic variations.

Paired sequencing data refers to a type of DNA sequencing where both ends of a DNA fragment are sequenced, resulting in two reads that are paired together.

An index of a genome sequence.|Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.

An index of data of biological relevance.

Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc.

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.|This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.

A DNA sequence.

The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule.|This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.

An identifier of a biological or bioinformatics database.

Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.

A structured query, in form of a script, that defines a database search task.

Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on.

Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network).

A report about a biosample.

An RNA sequence.

3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another.

Textual metadata on a software author or end-user, for example a person or other software.

An assembly of fragments of a (typically genomic) DNA sequence.|Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.

An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database.

Accession of a protein deposited in a database.

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.|This is a broad data type and is used a placeholder for other, more specific types.

Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects.|Variations are stored along with a reference genome.

An identifier of an entry from the PDB database.|A PDB identification code which consists of 4 characters, the first of which is a digit in the range 0 - 9; the remaining 3 are alpha-numeric, and letters are upper case only. (source: https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1996.pdf)

Data concerning a mass spectrometry measurement.

A phylogenetic tree that is an estimate of the character's phylogeny.

A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation.

A code number identifying a family from the CATH database.

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.

An informative report on intrinsic positional features of a protein sequence.|This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.

The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.|Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.

Accession of a peptide deposited in a database.

Annotation of positional sequence features, organised into a standard feature table.

Name of a protein.

Identifier of a pathway from the KEGG pathway database.

The name (or part of a name) of a file (of any type).

A unique identifier of a specific mutation catalogued in a database.

Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores.|This is the raw data produced by a DNA sequencing machine.