Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Will want to add a remark, and possibly a hyperlink, to/about a bulk data submission form/pipeline/spreadsheet | * Will want to add a remark, and possibly a hyperlink, to/about a bulk data submission form/pipeline/spreadsheet | ||
** What would be the best mechanism for bulk data submission? | ** What would be the best mechanism for bulk data submission? | ||
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| + | === Allele function ontology (ky)=== | ||
| + | * I could not find an ontology that was ready built to adopt; few genetic model organisms, of those, FB has the most useful. Other mods use controlled vocabularies (CVs) that either are not comprehensive enough (just has the basic null, loss of function, etc.) or molecular based (VariO, SO) | ||
| + | * made an ontology using Schedl defined terms and FB hierarchy | ||
| + | * Matt Brush of Monarch Initiative is making a GENO ontology (https://github.com/monarch-initiative/GENO-ontology genetic variation specified in genotypes, to support genotype-to-phenotype (G2P) data aggregation and analysis across diverse research communities and sources)for a cross-species genetic-based controlled vocabulary, I'll be submitting our terms to them, and modifying our terms to keep in sync with GENO. | ||
| + | * I've invited FB curators to work with us to make our terms species-nonspecific. | ||
Revision as of 16:46, 4 June 2015
Contents
Previous Years
2015 Meetings
June 2015
June 4, 2015
Allele-Phenotype Form
- Added link to Allele molecular lesion form (which currently also has phenotype submission fields)
- Added remark that optional fields apply to "ALL OBSERVED PHENOTYPES" for an allele
- Added link in WBPerson term info to Person page with publications showing
- Do we want individual e-mails sent out for each submission, or, say, one daily summary e-mail?
- The concern is that someone may abuse the form and send a bunch of junk to some random person's e-mail address
- Should confirmation e-mails contain a "I didn't submit this data" link to nullify abusive submissions? Would people use it?
- Do we want to set up a mechanism to block abusive IP addresses?
- Should we pre-populate the e-mail field once a user selects a name/WBPerson?
- It seems that many users want to enter data quickly and TAB away
- Do we want to allow exact matches to register even if a term is not selected from the autocomplete dropdown?
- Do we want a general free-text remark field for the entire submission? For individual optional fields?
- Will want to add a remark, and possibly a hyperlink, to/about a bulk data submission form/pipeline/spreadsheet
- What would be the best mechanism for bulk data submission?
Allele function ontology (ky)
- I could not find an ontology that was ready built to adopt; few genetic model organisms, of those, FB has the most useful. Other mods use controlled vocabularies (CVs) that either are not comprehensive enough (just has the basic null, loss of function, etc.) or molecular based (VariO, SO)
- made an ontology using Schedl defined terms and FB hierarchy
- Matt Brush of Monarch Initiative is making a GENO ontology (https://github.com/monarch-initiative/GENO-ontology genetic variation specified in genotypes, to support genotype-to-phenotype (G2P) data aggregation and analysis across diverse research communities and sources)for a cross-species genetic-based controlled vocabulary, I'll be submitting our terms to them, and modifying our terms to keep in sync with GENO.
- I've invited FB curators to work with us to make our terms species-nonspecific.
