kg-obo

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Duplicates in node list of PCO , version 2021-05-03,

1

### Describe the bug Duplicates in node list: ["PCO:0000030"]

LucaCappelletti94

Duplicates in node list of CHIRO, version 2015-11-23

1

### Describe the bug The provided graph name and version contains the following duplicated nodes: ["GO:0003824", "NCBITaxon:2"] ### To Reproduce Investigate node list. ## Expected behavior Node list should not...

LucaCappelletti94

Include transform of Biolink

3

## Describe the desired behavior In a KG construction crew meeting on Dec 12 2022, we discussed how it may be useful to have a topological representation of the Biolink...

caufieldjh

Update robot to newer version

1

It would be nice to use newer versions of `robot`, but... In #206, I saw that versions of `robot` newer than v1.8.3 appeared to break the transformation process, at least...

caufieldjh

**Name and description of the dataset** The [obo-db-ingest](https://github.com/biopragmatics/obo-db-ingest) exports OBO representations of frequently used knowledgebases (e.g., Reactome, UniProt, etc). **Dataset URL** [obo-db-ingest/export](https://github.com/biopragmatics/obo-db-ingest/tree/main/export) Download through PURLs, as in https://w3id.org/biopragmatics/resources/uniprot/2022_05/uniprot.obo.gz

caufieldjh

### Describe the bug Transform logs are saved to each output directory - see `tsv_transform.log` in [output like this](https://kg-hub.berkeleybop.io/kg-obo/ncbitaxon/2023-02-24/) - but these logs do not appear to contain KGX `validate`...

caufieldjh

### Describe the bug During stats generation, this error is raised: ``` 03:16:33 Downloading apollo_sv, version 2022-11-25 from KG-OBO: kg-obo/apollo_sv/2022-11-25/apollo_sv_kgx_tsv.tar.gz 03:16:33 Downloading apollo_sv, version v2023-01-10 from KG-OBO: kg-obo/apollo_sv/v2023-01-10/apollo_sv_kgx_tsv.tar.gz 03:16:33 Downloading...

caufieldjh

### Describe the bug Some compressed graph files contain directories, complicating automated processing. They are: ``` WBLS, 2022-09-22 WBLS, 2022-08-18 GNO, 2022-02-23 MOP, 2022-05-11 CHIRO, 2015-11-23 MMUSDV, 2020-03-10 BCO, 2021-11-14...

caufieldjh

**Name and description of the dataset** A slim of CHEBI is now available, with coverage of the majority of CHEBI classes used in OBO Foundry ontologies. **Dataset URL** [CHEBI OBO...

caufieldjh

### Describe the bug Some OBO transforms still have `OBO:` prefixes before their own prefixes. For example, `SCDO`: ``` id category name description provided_by synonym :http://www.w3.org/2004/02/skos/core#prefLabel accessRights accrualMethod accrualPeriodicity accrualPolicy...

caufieldjh