owlcollab / owlcollab/owltools
Correct label and biological process issues for model annotation loader, possible other improvements
@yy20716 is already working on this.
Since May 8, 2018.
- Dominant language
- Java
- Stars
- 115
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
Description
Looking at the output of a loader run: http://tomodachi.berkeleybop.org/amigo/search/model_annotation
The values in the return documents that drive this interface are like:
{
"document_category":"model_annotation",
"id":"gomodel:581e072c00000062|http://model.geneontology.org/581e072c00000062/581e072c00000098|FB:FBgn0005672|GO:0048019|",
"annotation_unit":"gomodel:581e072c00000062|http://model.geneontology.org/581e072c00000062/581e072c00000098|FB:FBgn0005672|GO:0048019|",
"annotation_unit_label":"gomodel:581e072c00000062 spi Dmel GO:0048019",
"annotation_unit_label_searchable":"gomodel:581e072c00000062 spi Dmel GO:0048019",
"model":"gomodel:581e072c00000062",
"model_label":"EGFR_SPI_DMEL",
"model_label_searchable":"EGFR_SPI_DMEL",
"model_label_searchable":"EGFR_SPI_DMEL",
"model_url":"http://noctua.berkeleybop.org/editor/graph/581e072c00000062.ttl",
"model_state":"development",
"model_date":"2016-11-07",
"model_date_searchable":"2016-11-07",
"model_date_searchable":"2016-11-07",
"enabled_by":"FB:FBgn0005672",
"enabled_by_searchable":"FB:FBgn0005672",
"enabled_by_label":"spi Dmel",
"enabled_by_label_searchable":"spi Dmel",
"enabled_by_label_searchable":"spi Dmel",
"function_class":"GO:0048019",
"function_class_label":"GO:0048019",
"function_class_label_searchable":"GO:0048019",
"function_class_label_searchable":"GO:0048019",
"function_class_closure_map":"{GO:0048019=null}",
"location_list_closure_map":"{GO:0005615=null}",
"owl_blob_json":"JSON_BLOB_REMOVED_FOR_BREVITY",
"evidence_type":"ECO:0000315",
"evidence_type_label":"ECO:0000315",
"evidence_type_label_searchable":"ECO:0000315",
"evidence_type_label_searchable":"ECO:0000315",
"evidence_type_closure_map":"{ECO:0000315=null}",
"reference":["PMID:7833286","PMID:7833286\t"],
"contributor":["http://orcid.org/0000-0003-3212-6364"],
"evidence_type_closure":["ECO:0000315"],
"reference_searchable":[
"PMID:7833286",
"PMID:7833286\t",
"PMID:7833286",
"PMID:7833286\t"],
"contributor_searchable":[
"http://orcid.org/0000-0003-3212-6364",
"http://orcid.org/0000-0003-3212-6364"],
"location_list_closure":["GO:0005615"],
"function_class_closure":["GO:0048019"],
"location_list":["GO:0005615"],
"location_list_label":["GO:0005615"],
"score":1.0
}
There are several oddities in this load:
- The
idandannotation_unitare generated as a pipe-separated combination of model id, M, P, and C; it seems that one of those is missing as there is a trailing pipe - all *
_searchablefields seem to be repeats; this may not be a "real" issue, practically speaking referenceandreference_searchableseem to contain tabs; they should not- all *
_closure_mapfields contain a "null", which would seem to indicate some issue with JSON deserialization or similar; the form should be id:label; note that this could merely be that there is something wrong with labels (see below) - for *
_label*, in almost all cases, there are no labels, just ids; it could be that the ontology information to get label is not loading properly as part of the command or something deeper - there should be a field set
process_class, just as there isfunction_class; no process fields exist
There are also a couple of issues that should be coordinated with other development, such as either switching to names for contributor (or making an id/label map), adding groups, etc.
While these may all be separate tickets, the tooling to get at the issues is similar for starters.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.