brunasv / issva

create OWL file for ISSVA classification

ISSVA

Project to create an OWL file for the ISSVA classification.

The International Society for the Study of Vascular Anomalies (ISSVA) is a multidisciplinary international society of physicians, scientists, and health care providers united by an interest in vascular anomalies. The Society aims to promote the highest standards of care for patients with vascular anomalies by advancing clinical and scientific knowledge concerning causes, diagnosis and treatment, and by education of physicians, health care providers, patients and the community. The Society encourages the free flow of information between its members and interested groups, through workshop meetings and teaching programs, and by the dissemination of a classification scheme and pertinent scientific data.

The updated classification was approved at the May, 2018 General Assembly in Amsterdam, the Netherlands.

https://bioportal.bioontology.org/ontologies/ISSVA

issva's Issues

Add causal genes as object properties instead of annotations

add coding?

define ISSVA ontology metadata

authors, license

VEGFR3 gene symbol

FLT4 is the approved gene symbol and already a gene in ISSVA as well. Can we remove VEGFR3 from ISSVA?

create description for ISSVA website

• what it is
• how to use (have to add to their databases, does not substitute classification)
• mention mappings to ordo
• contact issva for issue reporting

'Bannayan-Riley-Ruvalcaba syndrome' and PTEN

'Bannayan-Riley-Ruvalcaba syndrome' is the same as 'PTEN (type) hamartoma of soft tissue / "angiomatosis"

Organize List of Vascular Malformations order by rarity

currently:
Combined
Provisionally Unclassified
Simple
Major vessels
associated

should be:
Simple
Combined
Major Vessels
Associated.
Provisionally Unclassified

Add 2nd part of ISSVA terms to Protege ontology (page 8-13)

NCIT mapping url non-resolvable (on issva)

Fix plural / singular AVM labels

Maffucci Syndrome causal gene NPM11

I think is NPM1 and not NPM11 as stated in the ISSVA. Asked Leo https://pubmed.ncbi.nlm.nih.gov/26508204/

BioPortal URIs for SNOMED etc ?

Add labels to all classes + Fix plural / singular AVM labels

Some classes (e.g. arteries / veins) do not have a label yet

Glomulin gene symbol

in HUGO the approved gene symbol is GLMN. https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:14373
update in ISSVA? ask Leo

Cross-check list of PDF and Excel

• Terms
• Abbreviations
• Hierarchy

Vascular Anomalies of major named vessels

Check if we mapped correctly as ISSVA classification does (see slide 11 of ISSVA). That Vascular Anomalies of Major Named Vessels are Anomalies_of:

• origin
• course
• number
• length
• diameter (aplasia, hypoplasia, stenosis, ectasia/aneurysm)
• valves
• communication (AVF)
• persistence (of an embryonal vessel)

metadata bioportal

• add link to the pdf in bioportal
• update contact in bioportal to issva website contact (leo will provide)

update URLs?

Mappings: check skos:closeMatch vs skos:exactMatch choices

Add mappings to Protege ontology

• Use skos:exactMatch
• Use original URIs

Create ontology in Protege and upload to Github

Publish ontology to BioPortal

Gene mappings to HGNC

Add 1rst part of ISSVA terms to Protege ontology (page 2-7)

Malcavernin gene symbol

CCM2 is the approved gene symbol. Can we update in ISSVA?

causal relations

check causal relations gene-disease not appearing in bioportal

Add hierarchy / relations to Protege ontology