From 85b03fa0b011897fa1c61feccf541da35ea13767 Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Fri, 12 Jul 2024 15:30:44 -0600 Subject: [PATCH 1/2] Update gpad-gpi-2-0.md @balhoff , I *think* I made the changes in https://github.com/geneontology/go-annotation/issues/4881 about slashes in local ID and the relation list. I'm not sure how to accomplish > allow other properties but require values of known properties to match grammar in table Can you approve this, if correct, and make the remaining change, or make all the remaining changes in a new PR? --- specs/gpad-gpi-2-0.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/specs/gpad-gpi-2-0.md b/specs/gpad-gpi-2-0.md index 926f12c..9260d44 100644 --- a/specs/gpad-gpi-2-0.md +++ b/specs/gpad-gpi-2-0.md @@ -68,7 +68,7 @@ Header property | Example value | Comment | ------ | ------ | ------ | ------ | ------ | | 1 | DB_Object_ID | [ID](#ID)| `UniProtKB:P11678` | | | 2 | Negation | 'NOT'?| `NOT` | | -| 3 | Relation | [ID](#ID)| `RO:0002263` | The relation used MUST come from the [allowed gene-product-to-term relations](#allowed-gene-product-to-go-term-relations) | +| 3 | Relation | [ID](#ID)| `RO:0002263` | The relation used SHOULD come from the [allowed gene-product-to-term relations](#allowed-gene-product-to-go-term-relations) | | 4 | Ontology_Class_ID | [ID](#ID)| `GO:0050803` | The identifier MUST be a term from the GO ontology | | 5 | Reference | [ID](#ID) ( '\|' [ID](#ID) )*| `PMID:30695063` | Different IDs, e.g. PMID and MOD paper ID, MUST correspond to the same publication or reference | | 6 | Evidence_Type | [ID](#ID)| `ECO:0000315` | The evidence identifier MUST be a term from the ECO ontology. [GO evidence-ECO mapping file](https://purl.obolibrary.org/obo/eco/gaf-eco-mapping-derived.txt) | @@ -77,7 +77,7 @@ Header property | Example value | Comment | 9 | Annotation_Date | [Date_Or_Date_Time](#Date_Or_Date_Time)| `2019-01-30` | | | 10 | Assigned_By | [Prefix](#Prefix)| `MGI` | | | 11 | Annotation_Extensions | ( [Extension_Conj](#Extension_Conj) ( '\|' [Extension_Conj](#Extension_Conj) )* )?| `BFO:0000066(GO:0005829)` | | -| 12 | Annotation_Properties | ( [Property_Value_Pair](#Property_Value_Pair) ( '\|' [Property_Value_Pair](#Property_Value_Pair) )* )?| `contributor-id=orcid:0000-0002-1478-7671` | Properties and values MUST come conform to the list in [GPAD annotation properties](#gpad-annotation-properties) | +| 12 | Annotation_Properties | ( [Property_Value_Pair](#Property_Value_Pair) ( '\|' [Property_Value_Pair](#Property_Value_Pair) )* )?| `contributor-id=orcid:0000-0002-1478-7671` | Properties and values MUST conform to the list in [GPAD annotation properties](#gpad-annotation-properties) | ### GPI columns From a8bf52e40fabce89ce29339da14ab29545067d88 Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Fri, 12 Jul 2024 15:35:14 -0600 Subject: [PATCH 2/2] Update gpad-gpi-2-0.md --- specs/gpad-gpi-2-0.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specs/gpad-gpi-2-0.md b/specs/gpad-gpi-2-0.md index 9260d44..246fc7e 100644 --- a/specs/gpad-gpi-2-0.md +++ b/specs/gpad-gpi-2-0.md @@ -112,7 +112,7 @@ Header property | Example value | Comment | Property_Value | [Text](#Text)| | | ID | [Prefix](#Prefix) ':' [Local_ID](#Local_ID)| | | Prefix | [Alpha_Char](#Alpha_Char) [ID_Char](#ID_Char)*| The [GO database registry](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml) contains a list of valid prefixes that can be used in GPAD or GPI files. Every identifier prefix used in a GPAD or GPI file MUST have an entry in the registry. | -| Local_ID | ( [ID_Char](#ID_Char) \| ':' )+| | +| Local_ID | ( [ID_Char](#ID_Char) \| ':' \| '\/' )+| | | ID_Char | [Alpha_Char](#Alpha_Char) \| [Digit](#Digit) \| '_' \| '-' \| '.'| | | Date_Or_Date_Time | [Date](#Date) \| [Date_Time](#Date_Time)| | | Date | YYYY-MM-DD| Corresponds to [xsd:date](https://www.w3.org/TR/xmlschema-2/#date) without optional timezone (a subset of the ISO 8601 standard) |