Difference between revisions of "Neglected items"
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===Measurement value literals in OBD (including ranges)=== | ===Measurement value literals in OBD (including ranges)=== | ||
| − | Phenotypes that include a measurement are | + | Phenotypes that include a measurement are now stored without the measurement in OBD, for example "count" or "length" phenotypes. In Phenex, the user can choose a quality such as "length" for a phenotype, as in "basihyal bone" "length". The user can also input a literal numeric length in the measurement field (such as "11.5"), and also choose a unit from the unit ontology (such as "millimeters"). These values are not imported into OBD by the data loader. |
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===Measurement input interface supporting ranges for Phenex=== | ===Measurement input interface supporting ranges for Phenex=== | ||
Phenex supports input of a single number for measurements. Many publications provide ranges, which may or may not be bounded on both sides ("5-10", "more than 7"). | Phenex supports input of a single number for measurements. Many publications provide ranges, which may or may not be bounded on both sides ("5-10", "more than 7"). | ||
===Fully automated dataloader script=== | ===Fully automated dataloader script=== | ||
| − | The dataloader should run in an automated way on a server. It should be easy to install and run from any computer. ''I know Cartik is working on this but I'm not sure it's on a roadmap. --[[User:Jpb15|jim]] 15:53, 19 February 2009 (EST)'' | + | The dataloader should run in an automated way on a server. It should be easy to install and run from any computer. ''I know Cartik is working on this but I'm not sure it's on a roadmap. --[[User:Jpb15|jim]] 15:53, 19 February 2009 (EST)'' ''This is a high-priority item, in fact. The fact that it doesn't appear to be does indicate that it needs to be explicitly documented as such. --[[User:Hlapp|Hilmar]] 18:37, 19 February 2009 (EST)'' |
| + | |||
===Polymorphic matrix states in Phenex=== | ===Polymorphic matrix states in Phenex=== | ||
Data matrices sometimes use the NEXUS format for specifying polymorphic states. NeXML supports polymorphic state assignments, but Phenex doesn't provide any facilities for working with polymorphic states. | Data matrices sometimes use the NEXUS format for specifying polymorphic states. NeXML supports polymorphic state assignments, but Phenex doesn't provide any facilities for working with polymorphic states. | ||
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===Employing homology statements in data queries (via reasoning?)=== | ===Employing homology statements in data queries (via reasoning?)=== | ||
| − | We need to determine and explicitly document how homology annotations will impact reasoning related to phenotype annotation searches. | + | We need to determine and explicitly document how homology annotations will impact reasoning related to phenotype annotation searches. ''Phone call scheduled for April 2, 2009 to discuss --[[User:Pmabee@usd.edu|Pmabee@usd.edu]] 15:53, 31 March 2009 (EDT)'' |
==="Systematic character" PATO subset=== | ==="Systematic character" PATO subset=== | ||
| − | At the SICB 2009 meeting we discussed choosing a set of terms from PATO that would represent the "character attributes" we will standardly use to group phenotypes in a character matrix (in the web interface, for example). This subset should "bisect" the PATO ontology: any term should either be a descendant of, an ancestor of, or be, one and only one term in the systematic character slim. ''I believe Wasila and Paula have this on their agenda. --[[User:Jpb15|jim]] 16:15, 19 February 2009 (EST)'' | + | At the SICB 2009 meeting we discussed choosing a set of terms from PATO that would represent the "character attributes" we will standardly use to group phenotypes in a character matrix (in the web interface, for example). This subset should "bisect" the PATO ontology: any term should either be a descendant of, an ancestor of, or be, one and only one term in the systematic character slim. ''I believe Wasila and Paula have this on their agenda. --[[User:Jpb15|jim]] 16:15, 19 February 2009 (EST)'' Wasila & Paula proposed a list of PATO terms; Jim incorporated into new version of Phenote 3/20/09--[[User:Pmabee@usd.edu|Pmabee@usd.edu]] 15:53, 31 March 2009 (EDT) |
[[Category:Informatics]] | [[Category:Informatics]] | ||
Latest revision as of 13:37, 30 April 2009
This is a list of various items that have come up at meetings and other discussions, which don't seem to have made it onto any development plan or roadmap.
Contents
- 1 Measurement value literals in OBD (including ranges)
- 2 Measurement input interface supporting ranges for Phenex
- 3 Fully automated dataloader script
- 4 Polymorphic matrix states in Phenex
- 5 Search for phenotypes in web interface via anatomy part_of
- 6 Employing homology statements in data queries (via reasoning?)
- 7 "Systematic character" PATO subset
Measurement value literals in OBD (including ranges)
Phenotypes that include a measurement are now stored without the measurement in OBD, for example "count" or "length" phenotypes. In Phenex, the user can choose a quality such as "length" for a phenotype, as in "basihyal bone" "length". The user can also input a literal numeric length in the measurement field (such as "11.5"), and also choose a unit from the unit ontology (such as "millimeters"). These values are not imported into OBD by the data loader.
Measurement input interface supporting ranges for Phenex
Phenex supports input of a single number for measurements. Many publications provide ranges, which may or may not be bounded on both sides ("5-10", "more than 7").
Fully automated dataloader script
The dataloader should run in an automated way on a server. It should be easy to install and run from any computer. I know Cartik is working on this but I'm not sure it's on a roadmap. --jim 15:53, 19 February 2009 (EST) This is a high-priority item, in fact. The fact that it doesn't appear to be does indicate that it needs to be explicitly documented as such. --Hilmar 18:37, 19 February 2009 (EST)
Polymorphic matrix states in Phenex
Data matrices sometimes use the NEXUS format for specifying polymorphic states. NeXML supports polymorphic state assignments, but Phenex doesn't provide any facilities for working with polymorphic states.
Search for phenotypes in web interface via anatomy part_of
Currently the web interface and data service provide results using the is_a subsumption relation - searching for "bone" will return annotations to any particular bone. However we have not added a way to search for annotations to parts of some anatomical entity. This should already be supported by OBD - needs to be added to our query services and web interface.
Employing homology statements in data queries (via reasoning?)
We need to determine and explicitly document how homology annotations will impact reasoning related to phenotype annotation searches. Phone call scheduled for April 2, 2009 to discuss --Pmabee@usd.edu 15:53, 31 March 2009 (EDT)
"Systematic character" PATO subset
At the SICB 2009 meeting we discussed choosing a set of terms from PATO that would represent the "character attributes" we will standardly use to group phenotypes in a character matrix (in the web interface, for example). This subset should "bisect" the PATO ontology: any term should either be a descendant of, an ancestor of, or be, one and only one term in the systematic character slim. I believe Wasila and Paula have this on their agenda. --jim 16:15, 19 February 2009 (EST) Wasila & Paula proposed a list of PATO terms; Jim incorporated into new version of Phenote 3/20/09--Pmabee@usd.edu 15:53, 31 March 2009 (EDT)
