Skip to content

Latest commit

 

History

History
 
 

rules

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
ABOUT.md
ABOUT.md
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
SOP.md
SOP.md
 
 
gorule-0000001.md
gorule-0000001.md
 
 
gorule-0000002.md
gorule-0000002.md
 
 
gorule-0000003.md
gorule-0000003.md
 
 
gorule-0000004.md
gorule-0000004.md
 
 
gorule-0000005.md
gorule-0000005.md
 
 
gorule-0000006.md
gorule-0000006.md
 
 
gorule-0000007.md
gorule-0000007.md
 
 
gorule-0000008.md
gorule-0000008.md
 
 
gorule-0000009.md
gorule-0000009.md
 
 
gorule-0000010.md
gorule-0000010.md
 
 
gorule-0000011.md
gorule-0000011.md
 
 
gorule-0000013.md
gorule-0000013.md
 
 
gorule-0000014.md
gorule-0000014.md
 
 
gorule-0000015.md
gorule-0000015.md
 
 
gorule-0000016.md
gorule-0000016.md
 
 
gorule-0000017.md
gorule-0000017.md
 
 
gorule-0000018.md
gorule-0000018.md
 
 
gorule-0000019.md
gorule-0000019.md
 
 
gorule-0000020.md
gorule-0000020.md
 
 
gorule-0000021.md
gorule-0000021.md
 
 
gorule-0000022.md
gorule-0000022.md
 
 
gorule-0000023.md
gorule-0000023.md
 
 
gorule-0000024.md
gorule-0000024.md
 
 
gorule-0000025.md
gorule-0000025.md
 
 
gorule-0000026.md
gorule-0000026.md
 
 
gorule-0000027.md
gorule-0000027.md
 
 
gorule-0000028.md
gorule-0000028.md
 
 
gorule-0000029.md
gorule-0000029.md
 
 
gorule-0000030.md
gorule-0000030.md
 
 
gorule-0000031.md
gorule-0000031.md
 
 
gorule-0000032.md
gorule-0000032.md
 
 
gorule-0000033.md
gorule-0000033.md
 
 
gorule-0000035.md
gorule-0000035.md
 
 
gorule-0000036.md
gorule-0000036.md
 
 
gorule-0000037.md
gorule-0000037.md
 
 
gorule-0000038.md
gorule-0000038.md
 
 
gorule-0000039.md
gorule-0000039.md
 
 
gorule-0000042.md
gorule-0000042.md
 
 
gorule-0000043.md
gorule-0000043.md
 
 
gorule-0000044.md
gorule-0000044.md
 
 
gorule-0000045.md
gorule-0000045.md
 
 
gorule-0000046.md
gorule-0000046.md
 
 
gorule-0000047.md
gorule-0000047.md
 
 
gorule-0000048.md
gorule-0000048.md
 
 
gorule-0000049.md
gorule-0000049.md
 
 
gorule-0000050.md
gorule-0000050.md
 
 
gorule-0000051.md
gorule-0000051.md
 
 

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

GAF lines are parsed according to GAF 2.1 specifications

Each line of a GAF file is checked that it generally conforms to the GAF 2.1 spec and some GO specific specifications. The GAF 2.1 spec is here: http://geneontology.org/page/go-annotation-file-gaf-format-21.

Qualifier, evidence, aspect and DB object columns must be within the list of allowed values (as per the spec).

Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).

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. Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).

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.

Representation of binding in the GO

We use the term GO:0005515 and its children to represent instances of protein binding. If a gene G is annotated to this term, its function involves binding another protein. The partner protein is represented in the with/from field of the association, i.e. the 'evidence' is the partner protein. Annotation of gene G to a protein binding term requires that the partner protein also be annotated to a protein binding term, resulting in reciprocal protein binding annotations. Note that the specific protein binding term used for annotation does not have to be the same for each partner.

Note that this annotation rule predates the existence of annotation extensions (c16 in the GAF). It is more logical to specify the binding partner in c16, this would also allow cleaner separation of evidence from in-vivo activity, but for historic reasons the with/from field continues to be used.

This excludes GO:0042803 protein homodimerization activity GO:0051260 protein homooligomerization GO:0043621 protein self-association

Application to Noctua models

Discussion is ongoing, refer to: geneontology/molecular_function_refactoring#29

See Also

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.

Error report (number of errors) in [db_species]-report.html & owltools-check.txt (details).

IEP and HEP usage is restricted to terms from the Biological Process ontology

The IEP and its high thoughput equivalent, HEP, evidence codes are 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. Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).

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.

Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).

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.

Error report: .report.md

Annotation Intersection Alerts

Tools and rules for intersections/co-annotation checks in the Gene Ontology.

The report lives here http://snapshot.geneontology.org/reports/shared-annotation-check.html and is updated with each pipeline run.

Deprecated - PubMed reference formatting must be correct

DEPRECATED: This has been subsumed by GORULE:0000027

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; and only root nodes can have the evidence code ND.

The No Data (ND) evidence code should be only used for annotations to the root nodes: GO:0008150 biological_process, GO:0003674 molecular_function and GO:0005575 cellular_component.

The root nodes: GO:0008150 biological_process, GO:0003674 molecular_function and GO:0005575 cellular_component can only be annotated with the No Data (ND) evidence code.

Error report (number of errors) in [db_species]-report.html & owltools-check.txt (details).

Taxon-appropriate annotation check

GO taxon constraints ensure that annotations are not made to inappropriate species or sets of species. This information is obtained from the only_in_taxon and never_in_taxon tags in the ontology. See http://www.biomedcentral.com/1471-2105/11/530 for more details.

Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).

Deprecated. GO terms in annotations should not be obsolete.

This rule is now merged with GORULE:0000020.

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:0044419 : interspecies interaction between organisms' or the cellular component term 'GO:0044215 : other organism' as an ancestor.

With/From: 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.

Error report (number of errors) in [db_species]-report.txt & owltools-check.txt (details).

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.

Error report (number of errors) in [db_species]-report.txt & owltools-check.txt (details).

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:

Error report (number of errors) in [db_species]-report.html & owltools-check.txt (details).

Deprecated - Generic Reasoner Validation Check

DEPRECATED: This is done outside of the rules system. Ontobio performs a GAF -> RDF translation as part of the pipeline.

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

There should be no annotations to obsolete terms or to an alternate ID. Obsolete terms that have a replace_by tag and terms annotated to one of their alternative IDs (merged terms) will automatically be repaired to the valid term id. If no replacement is found, the annotation will be filtered.

Other GO terms present in annotations (with/from column, etc) also should be repaired if possible.

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.

Procedure

  • Any asserted or inferred annotation to MF, where MF part-of BP, will generate an involved-in to that BP
  • Any asserted or inferred annotation to BP, where BP occurs-in CC, will generate a part-of annotation to that CC

Evidence and provenance

  • Evidence, references, publications, date are retained
  • Assigned_by is GOC

TBD

Should this pipeline filter annotations based on some redundancy criteria?

Prevent propagation of certain terms by orthology

Prevent propagation of certain terms by orthology/similarity. This rule is under discussion

Creating more specific annotations by reasoning over extensions

Given an annotation to a general term plus annotation extensions we can infer a more specific annotation.

For example, given a source annotation:

Gene = geneA
Annotation_class = GO:0006260 ! DNA replication
Annotation_extension = {occurs_in GO:0000262 ! mitochondrial chromosome}

This will be inferred:

Gene = geneA
Annotation_class = GO:0006264 ! mitochondrial DNA replication
Annotation_extension = {occurs_in GO:0000262 ! mitochondrial chromosome}
Evidence: IC
With: GO:0006260

Approach is described in more detail here: https://github.com/owlcollab/owltools/wiki/Annotation-Extension-Folding

Fields:

  • GO ID: new inferred, more specific GO ID
  • Evidence: IC
  • With: original GO ID
  • Assigned-by: GOC-OWL

Other fields remain the same

IBA annotations must have been sourced from the PAINT inference pipeline

This seeks to filter out paint annotations that have leaked into the main mod GAF sources. In this way, we only have these paint annotations coming directly from paint.

If the GAF file being validated is not paint, and the line has evidence IBA, then throw out that line.

See also GORULE:0000037

Each identifier in GAF is valid

  • Col 1 and all DB abbreviations must be in db-xrefs.yaml (see below)
  • All GO IDs must be extant in current ontology

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/from" 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'

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

Aspect can only be one of C, P, F and should be repaired using the GO term

Aspect (Column 9) can be one either C, P, or F. These correspond to the three main branches of the Gene Ontology: C for Cellular Component, P for Biological Process, F for Molecular Function. These can be computed from the GO Term in the GAF annotation. If the Aspect is incorrect issue a warning and replace with the corrected aspect.

All IEAs over a year old are removed

All GAF annotations that have IEA as an evidence code that are also more than a year old should be removed.

Example: http://release.geneontology.org/2018-07-02/reports/gonuts-report.html 722 GO_AR:0000001 Error IEA evidence code present with a date more than a year old '20110217' UniProtKB P29430 pedA GO:0042742 GO_REF:0000004 IEA SP_KW:KW-0044 P protein taxon:1254 20110217 GONUTS

Deprecated GO_REFs are not allowed

GO_REFs are here: https://github.com/geneontology/go-site/tree/master/metadata/gorefs The following references are not allowed:

GO_REF:0000033 GO_PAINT:nnnnnnn (where n are digits)

Annotation relations are replaced when not provided by source

In GAFs, relation is overloaded into qualifier. If no explicit non-NOT qualifier is specified, use a default based on GPI specifications: For Cellular Component: relation = 'part_of' For Biological Process: relation = 'involved_in' For Molecular Function: relation = 'enables'

##This seems to be only exported in GPAD for now.

Allowed References for each ECO.

GO_REF Collection References allowed for each ECO are as follows: (to be completed)

Group specific Reference IDs (column 6) will be replaced by corresponding GO_REF (or other public ID) or filtered.

IDs in the Reference (column 6) field will only be accepted if they are from PMID, PMC, doi, or GO_REF. Group specific References will no longer be accepted and will be filtered. For example, FB:FBrf0159398 is a synonym for GO_REF:0000015. So if the FB Reference is found, it will be removed, leaving GO_REF:0000015 instead. If an ID cannot be repaired/replaced then the GAF annotation will be filtered.

The list of GO_REFs are here: https://github.com/geneontology/go-site/tree/master/metadata/gorefs.

'Colocalizes_with' qualifier not allowed with protein-containing complex (GO:0032991)' and children.

Report annotations that involve gene products where the gene product is annotated to a term 'x' and 'regulation of X' (multiple annotations involved)

Few proteins are part of a process as well as regulate that process. We need to review the list of proteins having annotations to a term x and to regulation of that term. This report would look globally at all annotations from any source and look for co-annotation of a term 'x' and its regulation ('regulation of X'). As a second step we may create exception lists for cases known to be correct.

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference

Only files coming from the https://github.com/geneontology/go-site/blob/master/metadata/datasets/paint.yaml can use the IBA evidence code.

If the evidence code is IBA, then (1) the assigned_by field must be GO_Central and (2) the reference field must be PMID:21873635.

Implementation: the GO Central pipeline should filter out IBAs from any submission source that is not a PAINT submission source, i.e. one registered in paint.yaml and having a name paint_X. Note that IBAs from PAINT will be injected in to the final release file for that organism.

Also see GORULE:0000026.

Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) where there exists another annotation with the same or a more granular term using experimental evidence

For annotations by ISO, ISA or ISS, the annotations of the gene product (col 8 info in the GAF) should be checked to ensure that an annotation exists to the same or a more granular term. For instance:

Gene Product 1 | GO:1233456 | ISS/ISO/ISA | with: Gene Product 2 Gene Product 2 | GO:1233456 (or a descentant) | EXP (or a descendant)

Allowed evidence codes for the primary annotations: EXP, IMP, IDA, IPI, IEP, IGI, HTP, HMP, HDA, HEP, HGI.

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

Annotations to GO:0032991 (protein-containing complex) or its descendants cannot refer to an identifer from ComplexPortal (Column 1). Example identifier:ComplexPortal:CPX-2158.

Qualifier: IKR evidence code requires a NOT qualifier

IKR evidence code requires a NOT qualifier.

Check for valid combination of evidence code and GO_REF

Specific forbidden combinations:

  • ND (ECO:0000307): GO_REF:0000015
  • ISS (ECO:0000250): GO_REF:0000024
  • ISA (ECO:0000247): GO_REF:0000030, GO_REF:0000113
  • ISM (ECO:0000255): GO_REF:0000030, GO_REF:0000050
  • ISO (ECO:0000266): GO_REF:0000024
  • IC (ECO:0000305): GO_REF:0000036, GO_REF:0000057, GO_REF:0000111
  • IKR (ECO:0000320): GO_REF:0000047
  • IDA (ECO:0000314): GO_REF:0000052, GO_REF:0000054 This list may not be exhaustive.

TODO: include above list in appropriate metadata file.

Reference: check for invalid use of GO_REF:0000057 can only be used with terms that are descendants of GO:0006915 (apoptotic process)

Reference: check for invalid use of GO_REF:0000057 can only be used with terms that are descendants of GO:0006915 (apoptotic process).

With/from: Verify that the combination of evidence (ECO) code and with/from conform to the rules in eco-usage-constraints.yaml

With/from: Verify that the combination of evidence (ECO) code and with/from conform to the rules in eco-usage-constraints.yaml

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms.

Annotations representing self-binding mean that the gene product annotated interacts with itself. Therefore, the entity in the 'with/from' column (colomn 8) should be the same as the gene product (column 2).

Self-binding terms include GO:0042803 protein homodimerization activity, GO:0051260 protein homooligomerization, GO:0051289 protein homotetramerization, GO:0070207 protein homotrimerization, GO:0043621 protein self-association, and GO:0032840 intramolecular proline-rich ligand binding (and their 'is_a' descendants).

With/from: ChEBI IDs in With/from can only be used with terms that are descendants of GO:0005488 (binding)

Annotations using a ChEBI ID in the with/from (col 8 of GAF) column should only be annotated with GO terms that are descendants of GO:0005488 (binding) (Col 5 of GAF)"

Gene products having ND annotations and other annotations in the same aspect should be reviewed

If a gene product has an annotation by the ND evidence code, this rule checks whether any manual annotations in the same GO aspect exists for this gene product.

If the annotation has 'contributes_to' as its qualifier, verify that at least one annotation to GO:0043234 (protein complex), or one of its child terms exists

The 'contributes to' qualifier can only be applied to proteins belonging to complexes, so any gene product with a MF annotation using the 'contributes to' should also be annotated to a child of protein complex.

Annotations to ISS, ISA and ISO should not be self-referential

Annotations to ISS, ISA and ISO should not have the same identifier in the 'gene product column' (column 2) and in the 'with/from' column (column 8).

Direct annotations to 'GO:0008283 cell population proliferation' require a value in the Annotation Extension field

Direct annotations to 'GO:0008283 cell population proliferation' require a value in the Annotation Extension field