Fungal NTRs: Perithecium development & Protoperithecium formation

[Achchuthan]

Accession: GO:xxxxxx
Name: Perithecium development
Ontology: biological_process
Definition: The process whose specific outcome is the progression of a perithecium over time, from its formation to the mature structure. Peritheicum is a flask-shaped fruiting body of certain molds and ascomycetous fungi having a pore for the escape of spores. In the ascomycetous fungi such as Neurospora crassa and Sordaria macrospora, these perithecia are formed in the sexual phase and they discharge ascospores through the ostiolum at the tip of the perithecial neck.
is_a: GO:0030582 ! reproductive fruiting body development
Source: BTO:0002164, PMID:125266, PMID:19547974, PMID:20739093, PMID:25311923, https://link.springer.com/chapter/10.1007/978-3-642-00286-1_2

Accession: GO:xxxxxx
Name: Protoperithecium formation
Ontology: biological_process
Synonyms: Primordium formation
Definition: The process of producing fruiting body precursors, called protoperithecia. Protoperitheicium is a spherical structure that is formed in the sexual phase of ascomycetous fungi such as Neurospora crassa and Sordaria macrospora. Protoperithecium is formed by the enveloping of ascogonia cells by sterile hyphae and it develops into perithecium.
Comment: Note that this term represents protoperithecium formation across homothallic and heterothallic species that do not have the same mechanism.
is_a: GO:0030582 ! reproductive fruiting body development
Source: PMID:125266, PMID:4410944, PMID:6235211, PMID:6235212, PMID:20739093, PMID:25311923, https://link.springer.com/chapter/10.1007/978-3-642-00286-1_2

[krchristie]

I have temporarily removed definition dbxrefs that were from BTO or were urls as they are violating a check for valid IDs in references:

:: ERROR: valid-id-space: bad id space 'BTO' in xref BTO:0002164
:: ERROR: valid-id-space: bad id space 'https' in xref https://link.springer.com/chapter/10.1007

@Achchuthan - Are these urls for DOI's? If so, then the appropriate format is like this:

DOI:10.1078/0176-1617-00593

@cmungall - What is needed to allow a BTO ID as a definition dbxref? BTO is a valid OBO Foundry ontology. Here's the link for the relevent BTO term:
http://www.ontobee.org/ontology/BTO?iri=http://purl.obolibrary.org/obo/BTO_0002164

[krchristie]

reopening until BTO issue is resolved

[krchristie]

@cmungall - There's a pull request to add an entry for BTO to db-xrefs.yaml:
geneontology/go-site#655

I'm not sure why it failed, or why I never saw an option to add you as a reviewer.

[krchristie]

Tried again (#15842) to put in BTO reference:

but still getting this error:
:: ERROR: valid-id-space: bad id space 'BTO' in xref BTO:0002164

[cmungall]

sorry I missed this the first time round. Merged, but will take a day to percolate.

I propose as a general principle for development terms

• we axiomatize using the appropriate ontology (FAO here)
• we don't reference an ontology term in the development term def xref as this is redundant (but FAO may choose to reference a BTO term if it chooses)

[cmungall]

FAO request: obophenotype/fungal-anatomy-ontology#19
Inquiry into status of FAO: obophenotype/fungal-anatomy-ontology#18