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Evidences

Introduction

Most information in UniProtKB has one or several “evidences” which describe the source of the information, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc.

Formally, an evidence is described by a mandatory evidence type, represented by a code from the Evidence Codes Ontology (ECO) and, where applicable, the source of the information, which is usually a database record (articles from the scientific literature are represented as PubMed records, but in the case of publications that are not in PubMed we indicate instead the corresponding UniProtKB reference number).

ECO comprises two high-level classes, evidence and assertion method. Evidence is defined as a type of information that is used to support an assertion and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be used to describe both the support for an assertion and whether that assertion was made by a human being or a computer. UniProtKB is using only codes that combine evidence and assertion method.

Here are some examples of how evidence descriptions look in the UniProtKB flat file format:

  • An evidence type without source: {type}, e.g.
    {ECO:0000305}
    {ECO:0000250}
    {ECO:0000255}
    
  • An evidence type with source: {type|source}, e.g.
    {ECO:0000269|PubMed:24356955}
    {ECO:0000303|Ref.6}
    {ECO:0000305|PubMed:22388736}
    {ECO:0000250|UniProtKB:P11497}
    {ECO:0000255|HAMAP-Rule:MF_03130}
    {ECO:0000256|HAMAP-Rule:MF_03130}
    {ECO:0000312|EMBL:AAY86039.1}
    {ECO:0000313|EMBL:AAY86039.1}
    {ECO:0000244|PDB:1V90}
    {ECO:0000213|PDB:1V90}
    
  • Several evidences: {type|source, type|source, ...}, e.g.
    {ECO:0000269|PubMed:10433554, ECO:0000303|Ref.6}
    

On the website, these descriptions are transformed to make them more user-friendly. The ECO codes are replaced by easy to understand labels and the sources are accessible by clicking on an arrow to list the hyper-linked sources. Evidences that are used in manual assertions are colored gold, e.g.

1 Publication By similarity UniRule annotation Imported

and those that are used in automatic assertions are colored blue, e.g.

UniRule annotation Imported

Evidence types that are used in UniProtKB

Evidences that are used only in manual assertions

Experimental evidence

We use the ECO code ECO:0000269 for manually curated information for which there is published experimental evidence. The PubMed identifier of the publication(s) which is the original source of the information is provided (for publications that are not in PubMed we indicate instead the corresponding UniProtKB reference number(s)).

Example: D9N129

1 Publication
CC   -!- FUNCTION: Together with wdr-48, binds to and stimulates the
CC       activity of the deubiquitinating enzyme usp-46, leading to
CC       deubiquitination and stabilization of the glr-1 glutamate
CC       receptor. {ECO:0000269|PubMed:24356955}.
Non-traceable author statement evidence

We use the ECO code ECO:0000303 for manually curated information that is based on statements in scientific articles for which there is no experimental support. The PubMed identifier of the paper(s) which is the original source of the information is provided (for publications that are not in PubMed we indicate instead the corresponding UniProtKB reference number(s)).

Example: Q24145

1 Publication
CC   -!- FUNCTION: May be involved in signal transduction on the apical
CC       surface of ectodermal epithelia regulating their polarity during
CC       invagination. Crumbs (crb) may be the intracellular signal.
CC       {ECO:0000303|PubMed:7892198}.
Curator inference evidence

We use the ECO code ECO:0000305 for manually curated information which has been inferred by a curator based on his/her scientific knowledge or on the scientific content of an article. If the information is inferred from the scientific content of an article, the PubMed identifier of the supporting paper is provided (for publications that are not in PubMed we indicate instead the corresponding UniProtKB reference number(s)).

Example: Q9UKV3

1 Publication
CC   -!- CAUTION: Structural and functional studies of the ASAP complex
CC       have been conducted with a chimeric complex involving a conserved
CC       fragment of Drosophila melanogaster Acinus/hkl.
CC       {ECO:0000305|PubMed:22388736}.

Example: P62196

1 Publication
FT   INIT_MET      1      1       Removed. {ECO:0000305|PubMed:16857966}.
Sequence similarity evidence

We use the ECO code ECO:0000250 for manually curated information which has been propagated from a related experimentally characterized protein. The accession number of the experimental source is provided (except for some historic UniProtKB/Swiss-Prot annotations, see Why do not all UniProtKB/Swiss-Prot annotations have evidences?).

Example: D3DJ41

By similarity
FT   MOD_RES     609    609       N6-biotinyllysine.
FT                                {ECO:0000250|UniProtKB:P11498}.

Evidences that are used in manual and automatic assertions

Sequence model evidence

We use the ECO code ECO:0000255 in manual assertions and ECO:0000256 in automatic assertions, respectively, for information which has been generated by the UniProtKB automatic annotation system. The database name and identifier of the sequence model rule that has been used by the system are provided.

Example: Q9W5X9

UniRule annotation PROSITE-ProRule annotations
CC   -!- SIMILARITY: Belongs to the acetyltransferase ATAT1 family.
CC       {ECO:0000255|HAMAP-Rule:MF_03130}.
CC   -!- SIMILARITY: Contains 1 N-acetyltransferase domain.
CC       {ECO:0000255|PROSITE-ProRule:PRU00532}.

Example: Q9VIC9

UniRule annotation UniRule annotation
CC   -!- CATALYTIC ACTIVITY: 10-formyltetrahydrofolate + NADP(+) + H(2)O =
CC       tetrahydrofolate + CO(2) + NADPH. {ECO:0000256|PIRNR:PIRNR036489}.
CC   -!- SIMILARITY: Belongs to the aldehyde dehydrogenase family.
CC       {ECO:0000256|RuleBase:RU003345}.

The ECO code ECO:0000255 is also used for information which has been generated by various sequence analysis programs that are used during the manual curation process and which has been verified by a curator.

Imported information evidence

We use the ECO code ECO:0000312 in manual assertions and ECO:0000313 in automatic assertions, respectively, for information which has been imported from another database. The database name and identifier of the entry from which the information has been imported are provided.

Example: Q4JIM5

Imported
GN   Name=Abl2 {ECO:0000312|EMBL:AAY86039.1, ECO:0000312|MGI:MGI:87860};

Example: Q2L9A9

Imported
GN   Name=Mdm2 {ECO:0000313|EMBL:ABC70327.1, ECO:0000313|MGI:MGI:96952};
Combinatorial evidence

We use the ECO code ECO:0000244 in manual assertions and ECO:0000213 in automatic assertions, respectively, for information inferred from a combination of experimental and computational evidence. It is currently used in UniProtKB for published large-scale proteomics data and a subset of 3D structural data for which UniProt makes use of computational procedures to generate the data. If the experimental evidence is derived from a paper, the PubMed identifier of the paper is provided. For experimental data derived from the Protein Data Bank, the PDB code is provided.

Example: P83256

Combined sources
FT   STRAND        5      7       {ECO:0000244|PDB:1V90}.
FT   TURN         11     13       {ECO:0000244|PDB:1V90}.
FT   STRAND       26     29       {ECO:0000244|PDB:1V90}.

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