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.

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

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.

Biological data that has been plotted as a graph of some type, or plotting instructions for rendering such a graph.

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 primary data itself.|You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.

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

An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc.

Data concerning the classification, identification and naming of organisms.|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.

Visualization of distribution of quantitative data, e.g. expression data, by histograms, violin plots and density plots.

A numerical value, that is some type of scored value arising for example from a prediction method.

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

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

3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure.|The coordinate data may be predicted or real.

Genetic variants are differences in DNA sequence that occur naturally among individuals in a population.

A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis.

An informative report about a DNA sequence assembly.|This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.

The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.|A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.

Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser.

A human-readable collection of information concerning a genome as a whole.

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

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

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

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 exluding the map(s) themselves. This includes metadata for map sets that share a common set of features which are mapped.

A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.|This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).

A table of unnormalized values representing summarised read counts per genomic region (e.g. gene, transcript, peak).

A mapping of supplied textual terms or phrases to ontology concepts (URIs).

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 context.

An informative report on protein-ligand (small molecule) interaction(s).

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

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 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).

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

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

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.

A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data.

Accession of an open reading frame (catalogued in a database).

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.

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 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.

The final processed (normalised) data for a set of hybridisations in a microarray experiment.|This combines data from all hybridisations.

A human-readable collection of information about the influence of genotype on drug response.|The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.

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 distinct from the primary data itself.

Alignment of exactly two molecular sequences.

Sequence map of a whole genome.

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.

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

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.