Request Ontology terms
Objectives
Outline the process of requesting ontology terms, as well as document release dates for the wrangler team.
Requesting new ontology terms
The way to request an ontology term depends on the type of term and whether it already exists in another ontology. A decision tree to guide you on the method for requesting a term can be found here: Ontology requests decision tree.
In general you should try to include as much information as possible when requesting a term. Specific cases are provided below.
General guidance for all ontologies
- Indicate your use case
- Indicate the evidence for your term such as a publication or link to description
- tag @zoependlington in the ticket and label the ticket with
HCAif possible - Indicate priority if urgent
- Use the applicable issue template
Ontology requests should be issued as tickets on the relevant repo to that ontology, see listing below.
If you aren’t sure about what to do or have an ontology question, create a ticket in the HCAO ontology repo.
For Cell type (CL) and Anatomical (UBERON) terms
As above for all ontology terms plus:
- Check whether the term exists in FMA, if so, please include the FMA ID in the definition section of the issue template
- Quote a publication or literature and evidence to support the term
- tag @zoependlington in the ticket
- Indicate any known taxon restrictions i.e. is the term only applicable to mammals? Quote literature if possible
For Experimental Factor (EFO) terms
As above for all ontology terms plus:
- Check whether the term exists in BAO, if so, please include the BAO ID in the definition section of the issue template
- Include a link to the literature if possible
Requesting an existing term be added to the HCAO
If the term already exists in an ontology that can be imported into the HCAO, make a ticket directly in the HCAO repo.
Release dates and plan of release
The tickets added to the ontology repository, as posted above, are revised by @zoependlington after tagging. Depending on your request:
- New term request: Terms should be requested by the 10th of each month*.
- Import of terms from other ontologies into HCAO: Up until the 17th of each month.
*New terms might not be available after each monthly release if requesting to an external database (Not EFO).
Release of databases:
- EFO = ~15-18th of each month.
- HCAO = ~20th of each month.
Once Zoe updates the HCAO it gets automatically released to the EBI OLS. She will usually ping the ingest team to also release the ontology to our environments on:
Ontology-related questions
For any question, please contact @zoependlington or @paolaroncaglia. Tickets in the HCAO repo are preferred for complex ontology questions.
Please take in account that she is only working 20% for the HCA, so be patient with your requests.
Ontology repos
| Field type | Ontology | github repo |
|---|---|---|
| Anatomical location | Uber-anatomy ontology (UBERON) | obophenotype/uberon |
| Cell types | Cell ontology (CL) | obophenotype/cell-ontology |
| Experimental factors & Developmental stage (mouse) | Experimental Factor Ontology (EFO) | EBISPOT/efo |
| Ethnicity | Human Ancestry Ontology (HANCESTRO) | EBISPOT/ancestro |
| Developmental stage (human) | Human Developmental Stages (HSAPDV) | obophenotype/developmental-stage-ontologies |
| Diseases | Mondo Disease Ontology (MONDO) | monarch-initiative/mondo |
| File content | Bioinformatics operations, data types, formats, identifiers and topics (EDAM) | edamontology/edamontology |
| Chemicals & Molecules | Chemical Entities of Biological Interest (CHEBI) | ebi-chebi/ChEBI |
| Imaging techniques | Biological Imaging Methods Ontology (FBBI) | CRBS/Biological_Imaging_Methods_Ontology |