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README.md

GO Rules

This folder contains the metadata for all annotation and ontology QC rules in GO. Each rule has an identifier, metadata and descriptions. Some rules are automatable, in which case the metadata contains the information required to execute it.

For more details for GOC members on how to create rules, see SOP.md

Basic GAF checks

The following basic checks ensure that submitted gene association files conform to the GAF spec, and come from the original GAF check script.

  • Each line of the GAF file is checked for the correct number of columns, the cardinality of the columns, leading or trailing whitespace
  • Col 1 and all DB abbreviations must be in db-xrefs.yaml (see below)
  • All GO IDs must be extant in current ontology
  • Qualifier, evidence, aspect and DB object columns must be within the list of allowed values
  • DB:Reference, Taxon and GO ID columns are checked for minimal form
  • Date must be in YYYYMMDD format
  • All IEAs over a year old are removed
  • Taxa with a 'representative' group (e.g. MGI for Mus musculus, FlyBase for Drosophila) must be submitted by that group only

Additional notes on identifiers

In some contexts an identifier is represented using two fields, for example col1 (prefix) and col2 (local id) of a GAF or GPAD. The global id is formed by concatenating these with :. In other contexts such as the "With/fron" field, a global ID is specified, which MUST always be prefixed.

In all cases, the prefix MUST be in db-xrefs.yaml. The prefix SHOULD be identical (case-sensitive match) to the database field. If it does not match then it MUST be identical (case-sensitive) to one of the synonyms.

When consuming association files, programs SHOULD repair by replacing prefix synonyms with the canonical form, in addition to reporting on the mismatch. For example, as part of the association file release the submitted files should swap out legacy uses of 'UniProt' with 'UniProtKB'

No 'NOT' annotations to 'protein binding ; GO:0005515'

Even if an identifier is available in the 'with' column, a qualifier only informs on the GO term, it cannot instruct users to restrict the annotation to just the protein identified in the 'with', therefore an annotation applying protein binding ; GO:0005515 with the not qualifier implies that the annotated protein cannot bind anything.

This is such a wide-reaching statement that few curators would want to make.

This rule only applies to GO:0005515; children of this term can be qualified with not, as further information on the type of binding is then supplied in the GO term; e.g. not + NFAT4 protein binding ; GO:0051529 would be fine, as the negative binding statement only applies to the NFAT4 protein.

For more information, see the binding guidelines on the GO wiki.

Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field

Annotations to binding : GO:0005488 or protein binding ; GO:0005515 with the TAS, NAS, IC, IMP, IGI and IDA evidence codes are not informative as they do not allow the interacting partner to be specified. If the nature of the binding partner is known (protein or DNA for example), an appropriate child term of binding ; GO:0005488 should be chosen for the annotation. In the case of chemicals, ChEBI IDs can go in the 'with' column. Children of protein binding ; GO:0005515 where the type of protein is identified in the GO term name do not need further specification.

For more information, see the binding guidelines on the GO wiki.

Reciprocal annotations for 'protein binding ; GO:0005515'

When annotating to terms that are descendants of protein binding, and when the curator can supply the accession of the interacting protein accession, it is essential that reciprocal annotations are available - i.e. if you say protein A binds protein B, then you need to also have the second annotation that states that protein B binds protein A.

This will be a soft QC; a script will make these inferences and it is up to each MOD to evaluate and include the inferences in their GAF/DB.

For more information, see the binding guidelines on the GO wiki.

No ISS or ISS-related annotations to 'protein binding ; GO:0005515'

If we take an example annotation:

gene product: protein A
GO term: protein binding ; GO:0005515
evidence: IPI
reference: PMID:123456
with/from: with protein A

this annotation line can be interpreted as: protein A was found to carry out the 'protein binding' activity in PMID:12345, and that this function was Inferred from the results of a Physicial Interaction (IPI) assay, which involved protein X

However if we would like to transfer this annotation to protein A's ortholog 'protein B', the ISS annotation that would be created would be:

gene product: protein B
GO term: protein binding ; GO:0005515
evidence: ISS
reference: GO_REF:curator_judgement
with/from: with protein A

This is interpreted as 'it is inferred that protein B carries out protein binding activity due to its sequence similarity (curator determined) with protein A, which was experimentally shown to carry out 'protein binding'.

Therefore the ISS annotation will not display the the interacting protein X accession. Such an annotation display can be confusing, as the value in the 'with' column just provides further information on why the ISS/IPI or IGI annotation was created. This means that an ISS projection from protein binding is not particularly useful as you are only really telling the user that you think an homologous protein binds a protein, based on overall sequence similarity.

This rule only applies to GO:0005515, as descendant terms such as mitogen-activated protein kinase p38 binding ; GO:0048273 used as ISS annotations are informative as the GO term name contains far more specific information as to the identity of the interactor.

For more information, see the binding guidelines on the GO wiki.

IEP usage is restricted to terms from the Biological Process ontology

The IEP evidence code is used where process involvement is inferred from the timing or location of expression of a gene, particularly when comparing a gene that is not yet characterized with the timing or location of expression of genes known to be involved in a particular process. This type of annotation is only suitable with terms from the Biological Process ontology.

For more information, see the binding guidelines on the GO wiki.

IPI should not be used with catalytic activity molecular function terms

The IPI (Inferred from Physical Interaction) evidence code is used where an annotation can be supported from interaction evidence between the gene product of interest and another molecule (see the evidence code documentation). While the IPI evidence code is frequently used to support annotations to terms that are children of binding ; GO:0005488, it is thought unlikely by the Binding working group that enough information can be obtained from a binding interaction to support an annotation to a term that is a chid of catalytic activity ; GO:0003824. Such IPI annotations to child terms of catalytic activity ; GO:0003824 may need to be revisited and corrected.

For more information, see the catalytic activity annotation guide on the GO wiki.

No annotations should be made to uninformative high level terms

Some terms are too high-level to provide useful information when used for annotation, regardless of the evidence code used.

We provide and maintain the list of too high-level terms as two subsets in the ontology:

  • gocheck_do_not_annotate "Term not to be used for direct annotation"
  • gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"

Both subsets denote high level terms, not to be used for any manual annotation.

For inferred electronic annotations (IEAs), we allow the use of terms from the gocheck_do_not_manually_annotate subset. These terms may still offer some general information, but a human curator should always be able to find a more specific annotation.

Annotation Intersection Alerts

To be added

PubMed reference formatting must be correct

References in the GAF (Column 6) should be of the format db_name:db_key|PMID:12345678, e.g. SGD_REF:S000047763|PMID:2676709. No other format is acceptable for PubMed references; the following examples are invalid:

  • PMID:PMID:14561399
  • PMID:unpublished
  • PMID:.
  • PMID:0

This is proposed as a HARD QC check: incorrectly formatted references will be removed.

ND annotations to root nodes only

The No Data (ND) evidence code should be used for annotations to the root nodes only and should be accompanied with GO_REF:0000015 or an internal reference. PMIDs cannot be used for annotations made with ND.

  • if you are using an internal reference, that reference ID should be listed as an external accession for GO_REF:0000015. Please add (or email) your internal reference ID for GO_REF:0000015.
  • All ND annotations made with a reference other than GO_REF:0000015 (or an equivalent internal reference that is listed as external accession for GO_REF:0000015) should be filtered out of the GAF.

The SQL code identifies all ND annotations that do not use GO_REF:0000015 or one of the alternative internal references listed for it in the GO references file.

Taxon-appropriate annotation check

GO taxon constraints ensure that annotations are not made to inappropriate species or sets of species. See http://www.biomedcentral.com/1471-2105/11/530 for more details.

Valid GO term ID

This check ensures that the GO IDs used for annotations are valid IDs and are not obsolete.

Dual species taxon check

Dual species annotations are used to capture information about multi-organism interactions. The first taxon ID should be that of the species encoding the gene product, and the second should be the taxon of the other species in the interaction. Where the interaction is between organisms of the same species, both taxon IDs should be the same. These annotations should be used only in conjunction with terms that have the biological process term 'GO:0051704 : multi-organism process' or the cellular component term 'GO:0044215 : other organism' as an ancestor.

IC annotations require a With/From GO ID

All IC annotations should include a GO ID in the "With/From" column; for more information, see the IC evidence code guidelines.

IDA annotations must not have a With/From entry

Use IDA only when no identifier can be placed in the "With/From" column. When there is an appropriate ID for the "With/From" column, use IPI.

IPI annotations require a With/From entry

All IPI annotations should include a nucleotide/protein/chemical identifier in the "With/From" column (column 8). From the description of IPI in the GO evidence code guide: "We strongly recommend making an entry in the with/from column when using this evidence code to include an identifier for the other protein or other macromolecule or other chemical involved in the interaction. When multiple entries are placed in the with/from field, they are separated by pipes. Consider using IDA when no identifier can be entered in the with/from column." All annotations made after January 1 2012 that break this rule will be removed.

Generic Reasoner Validation Check

The entire GAF is converted to OWL, combined with the main GO ontology and auxhiliary constraint ontologies. The resulting ontology is checked for consistency and unsatisfiable classes over using a complete DL reasoner such as HermiT.

Automatic repair of annotations to merged or obsoleted terms

Ontology operations such as term merges and obsoletions may be out of sync with annotation releases. Each GO entry T in the GAF is checked to see if it corresponds to a valid (non-obsolete) term in the ontology. If not, metadata for other terms is checked. If the term has been merged into a term S (i.e. S has alt_id of T) then T is replaced by S in the GAF line.

Check with/from for sequence similarity evidence for valid database ID

For ISS and related evidence types, the With/From field should point to a valid gene or gene product identifier that is annotated with a GO term that is either identical to or a descendant of the main annotation.

Check for, and filter, annotations made to retracted publications

GO should not include annotations to retracted publications. PubMed keeps record of retracted publications in the PublicationTypeList of each paper's XML entry. For additional details on this proposed rule, please see: geneontology/go-annotation#1479

Materialize annotations for inter-branch links in the GO

Annotations will be propagated from MF to BP over part_of, or from BP to CC over occurs_in.

Background

Historically GO treated MF, BP and CC as distinct ontologies. They are now better regarded as branchers or sub-hierarchies within a single ontology, cross-linked via a variety of relations. Annotators used to make manual duplicate annotations.

TBD

Should this pipeline filter annotations based on some redundancy criteria?