Closed mastevb closed 2 years ago
Added delay for processing so the user can finish typing and not fire up multiple search queries.
implemented in: https://github.com/sys-bio/vscode-antimony/commit/dee492ac73e22b247ef5e7739cfbc2589d20bb69
Added progress report bar and notification for no results found.
implemented in https://github.com/sys-bio/vscode-antimony/commit/c378a0a8828b09ec050303e72b66839657824bba
bulk insert chebis from 'chebi.csv'
with (ROWTERMINATOR = '0x0a', FIELDTERMINATOR = '~QwQ~', FIELDQUOTE = '!',
DATA_SOURCE = 'blob2', FORMAT='CSV', CODEPAGE = 65001, --UTF-8 encoding
FIRSTROW=1,TABLOCK);
CREATE INDEX index1 ON [dbo].[chebis] (name);
import xmltodict
import csv
contents = open("chebi.xml").read()
ch = xmltodict.parse(contents)
chebis = ch["rdf:RDF"]["owl:Class"]
f = open("chebi.csv", "w")
for chebi in chebis:
if "rdfs:label" in chebi.keys() and "oboI:id" in chebi.keys():
text = chebi["rdfs:label"]['#text']
id = chebi["oboI:id"]['#text']
f.write("!{}!~QwQ~!{}!\n".format(text, id))
Also need to improve the mapping between types and variables and the database to choose from
For SBML compartments, support searching Gene Ontology:cellular component Cell Type Ontology Foundational Model of Anatomy Mouse Adult Gross Anatomy Ontology for Biomedical Investigations
For SBML species, support searching ChEBI Protein Ontology UniProt
For SBML reactions, support searching GO:biological process RHEA
Hi Steve,
Here's a link to the OMEX metadata specification that I mentioned today: https://doi.org/10.1515/jib-2021-0020
If you jump to section 2.4.2 (Resources to use for composite semantic annotations) there is a list of recommended ontologies and databases there.
Working from that list, I would recommend you support searches for the following SBML components like so:
For SBML compartments, support searching Gene Ontology:cellular component Cell Type Ontology Foundational Model of Anatomy Mouse Adult Gross Anatomy Ontology for Biomedical Investigations
For SBML species, support searching ChEBI Protein Ontology UniProt
For SBML reactions, support searching GO:biological process RHEA
This recommendation is based on what's in the OMEX metadata specification, which was created with a particular user community in mind. Your target users might have other ontologies or databases that they want to be able to search. For example, some people like to use KEGG, but it's proprietary and so isn't included in the recommended resources in the OMEX metadata spec. Just something to keep in mind.
Hope this is helpful.
M
Currently, creating annotations rely on a third-party package for retrieving annotation information from several sources. There are two problems with this approach:One idea is to transform all of the data to our own cloud-based database and query from there, but since this will require some sort of funding, we need some data to back our claim:
and also https://github.com/sys-bio/vscode-antimony/issues/48