PO PlantSystematics conference call 10-21-11 - Revision history

Rwalls at 21:59, 21 October 2011

2011-10-21T21:59:27Z

Rwalls at 21:50, 21 October 2011

2011-10-21T21:50:47Z

Rwalls at 18:53, 21 October 2011

2011-10-21T18:53:40Z

Rwalls: Created page with 'Meeting to discuss technical issues of linking between PO and PS.org.'

2011-10-21T16:42:09Z

Created page with 'Meeting to discuss technical issues of linking between PO and PS.org.'

New page

Meeting to discuss technical issues of linking between PO and PS.org.

@@ Line 3: / Line 3: @@
 Present: Kevin Nixon, Pankaj Jaiswal, Justin Elser, Justin Preece, Ramona Walls
+==notes from meeting==
 JP: Currently no way of automatically putting in links to keywords -- means manual curation, which is time consuming and can lead to errors.
@@ Line 31: / Line 31: @@
 PJ:  (side note) working on software (with collaborator at OSU) to build sectors on images and automatically identify what is on image based on a library.
-We have two needs: 1. link to images from PO 2. link all PSO images to PO IDs.
+'''We have two needs: 1. link to PS.org images from PO 2. link PS.org images to PO IDs.'''
 KN: First step is to implement a search that is sufficient given existing data structure, then move toward system that integrates PO by downloading a table from PO that integrates with his terms.
@@ Line 63: / Line 63: @@
 May also need to think about window dimension later, if we decide to incorporate a pop-up from PO site.

@@ Line 1: / Line 1: @@
 Meeting to discuss technical issues of linking between PO and PS.org.
-JP: no way of automatically putting in links to keywords automatically
+Present: Kevin Nixon, Pankaj Jaiswal, Justin Elser, Justin Preece, Ramona Walls
-Kevin can have access to this
+JP: Currently no way of automatically putting in links to keywords -- means manual curation, which is time consuming and can lead to errors.
-If an image on PS.o has an association to PO, we can have an automatic association
+PJ: if we had a list of keywords, we could create a mapping and just maintain that, then use that mapping to create links both from PO to PS.org and from PS.org to PO
-Mapping: connect to 1000 image for petal. Don't want to create xrefs for all of them.
+Mapping could be hosted on PO SVN site. We have a mappings folder already. SN can have access to this.
-Contributors don't always put in keywords.
+If an image on PS.org has an association to PO, we can could use that to automaticly create associations.
-KN create a table of keywords and ID, we keep them updated with our list of ids
+Advantage of mapping/using keywords rather than links to individual images: Don't want to create xrefs for keywords (like flower) that have hundreds of images.
-Can't do boolean search, but we could send him list of words which he could then split out and turn into wildcards to separate terms. No need for any additional association file or mappings.
+PS.org presently can't do boolean search. PO could input a list of words which PS.org could then split out  into separate terms, and add wildcards. No need for any additional association file or mappings.
-KN could add flag to images. We could click on which images we want.
+KN could add flags to images that match keywords, then we could click on which images we want to keep -- to avoid false positives.
-We have two needs: 1. link to images from PO 2. link all PSO images to PO IDs.
+KN create a table of keywords and ID, we keep them updated with our list of ids
-We are trying to encourage people to use standard vocabulary.
+PO is trying to encourage people to use standard vocabulary -- this is why we want to have links to PO terms/IDs.
 Could begin mappings, but still have fuzzy search that will complement this.
-PJ: we are working on software to build sectors on images and automatically identify what is on image based on a library.
+PJ:  (side note) working on software (with collaborator at OSU) to build sectors on images and automatically identify what is on image based on a library.
 KN: First step is to implement a search that is sufficient given existing data structure, then move toward system that integrates PO by downloading a table from PO that integrates with his terms.
@@ Line 34: / Line 37: @@
 KN can start by sending us a list of his keywords. But many of them won't be relevant for PO.
-Need a mechanism in place so that additions and changes are updated automatically as much as possible.
+PO will use this to create a mapping file.
-RW and KN can start with only terms associated with ie flower and leaf to see how far we can extend from there.
+Need to have a mechanism in place so that additions and changes are updated automatically as much as possible.
 Start by getting keywords from KN and doing a candidate mapping.
@@ Line 42: / Line 47: @@
 Standard format of mapping file is on SVN -- we will use same format.
-We are using UTF8 (not unicode) - current AmiGO is UTF, but we may go to unicode
+PO is using UTF8 (not unicode) because AmiGO requires UTF, but we may go to unicode in the future.
-FAO is translating ontology into different languages.
+KN: IP for pages on PS.org will be moving, so we want to stick with www.plantsystematics domain - going onto gigabit server.
 KN: list of keywords, work on search function and give us a different url for it.
+We will input a list of words, delimited however we want (& or whatever) and KN will write a query that takes those and does a fuzzy search on them then create the link to the correct search results page (he has something like this he has already used for taxonomic names - works with missing letter and internal errors - can transfer this over to keyword search, even though he hasn't done it yet)
 Will need to figure out what delimiter to use to separate words: e.g., stamen&anther&filament
-May want to have something like po_word:something;taxon:something
+May want to have something like po_word:
-We can always add other variables later when want.
+Eventually, we could add other variables, like: po_word:something;taxon:something.
-May need to think about window dimension later, if we can incorporate a popup from PO site.
+May also need to think about window dimension later, if we decide to incorporate a pop-up from PO site.

← Older revision		Revision as of 18:53, 21 October 2011
Line 1:		Line 1:
	Meeting to discuss technical issues of linking between PO and PS.org.		Meeting to discuss technical issues of linking between PO and PS.org.
		+
		+	JP: no way of automatically putting in links to keywords automatically
		+
		+	PJ: if we had a list of keywords, we can create a mapping and just maintain that
		+
		+	Mapping should be hosted on PO SVN site. We have a mappings folder already.
		+
		+	Kevin can have access to this
		+
		+	If an image on PS.o has an association to PO, we can have an automatic association
		+
		+	Mapping: connect to 1000 image for petal. Don't want to create xrefs for all of them.
		+
		+	Contributors don't always put in keywords.
		+	could have students etc. upgrade that
		+
		+	KN create a table of keywords and ID, we keep them updated with our list of ids
		+
		+	Can't do boolean search, but we could send him list of words which he could then split out and turn into wildcards to separate terms. No need for any additional association file or mappings.
		+
		+	KN could add flag to images. We could click on which images we want.
		+
		+	We have two needs: 1. link to images from PO 2. link all PSO images to PO IDs.
		+
		+	We are trying to encourage people to use standard vocabulary.
		+
		+	Could begin mappings, but still have fuzzy search that will complement this.
		+
		+	PJ: we are working on software to build sectors on images and automatically identify what is on image based on a library.
		+
		+	KN: First step is to implement a search that is sufficient given existing data structure, then move toward system that integrates PO by downloading a table from PO that integrates with his terms.
		+
		+	KN can start by sending us a list of his keywords. But many of them won't be relevant for PO.
		+
		+	Need a mechanism in place so that additions and changes are updated automatically as much as possible.
		+
		+	RW and KN can start with only terms associated with ie flower and leaf to see how far we can extend from there.
		+
		+	Start by getting keywords from KN and doing a candidate mapping.
		+
		+	Standard format of mapping file is on SVN -- we will use same format.
		+
		+	We are using UTF8 (not unicode) - current AmiGO is UTF, but we may go to unicode
		+
		+	FAO is translating ontology into different languages.
		+
		+	IP will be moving, so we want to stick with www.plantsystematics domain - going onto gigabit
		+
		+	Could start with all images that have keyword flower and any keyword associated with it.
		+
		+	Because he is using frames will have to something
		+
		+	KN: list of keywords, work on search function and give us a different url for it.
		+
		+
		+	We will send a list of words, delimited however we want (& or whatever) and KN will write a query that takes those and do a fuzzy search on them then (he has something like this he has already used for taxonomic names - works with missing letter and internal errors - can transfer this over to keyword search, even though he hasn't done it yet)
		+
		+	Will need to figure out what delimiter to use to separate words: e.g., stamen&anther&filament
		+
		+	May want to have something like po_word:something;taxon:something
		+
		+	We can always add other variables later when want.
		+
		+	May need to think about window dimension later, if we can incorporate a popup from PO site.