SDIWG:Action Items 20081219 - Revision history

Noy: /* Biositemaps Web-Services Specifications */

2009-01-22T19:38:05Z

Biositemaps Web-Services Specifications

Noy: /* II. Information Model (IM) */

2009-01-22T19:37:44Z

II. Information Model (IM)

Noy: /* I. Biomedical Resource Ontology (BRO) ontology */

2009-01-22T19:35:52Z

I. Biomedical Resource Ontology (BRO) ontology

Ivo at 21:32, 16 January 2009

2009-01-16T21:32:57Z

Bkirschn at 19:29, 16 January 2009

2009-01-16T19:29:51Z

Ivo: /* Important Note */

2009-01-16T19:01:12Z

Important Note

Ivo at 18:25, 16 January 2009

2009-01-16T18:25:43Z

Bkirschn at 15:41, 16 January 2009

2009-01-16T15:41:18Z

Ivo: /* iTools processing (consumption/production) of Biositemaps.RDF */

2009-01-14T23:54:53Z

iTools processing (consumption/production) of Biositemaps.RDF

Ivo: /* iTools processing (consumption/production) of Biositemaps.RDF */

2009-01-14T23:54:05Z

iTools processing (consumption/production) of Biositemaps.RDF

@@ Line 65: / Line 65: @@
 ** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode
 ** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)
-*** Note [NN]: This call is very ambiguous in case of multiple inheritance. We suggest to use getParents and then call get Children for each of the parents to get appropriate sets of siblings. We agreed on 1/12 to defer the issue for now.
+*** Note [NN]: This call is very ambiguous in case of multiple inheritance. We suggest to use getParents and then call get Children for each of the parents to get appropriate sets of siblings. We agreed on January 16, 2009 to defer the issue for now.
 ===II. Information Model (IM)===

@@ Line 70: / Line 70: @@
 * http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:
 ** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html
 ** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".
 ** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"
 ** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.

@@ Line 60: / Line 60: @@
 ** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)
 ** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many
 ** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode
 ** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode
 ** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)
 ===II. Information Model (IM)===

← Older revision		Revision as of 21:32, 16 January 2009
Line 92:		Line 92:

	: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''		: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''
		+
		+	==[[SDIWG:Action_Items_20090116\| See Follow up notes]]==

@@ Line 9: / Line 9: @@
 ** Action: Ivo - weekly update of iTools already done
 ** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)
-** Action: Beth - registration form for adding biositemaps to registry
+** Action: Beth - <strike>registration form for adding biositemaps to registry</strike> (done)
 ** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)
 ** Action: Csongor - browseable mode for biositemaps editor

← Older revision		Revision as of 19:01, 16 January 2009
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	: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''		: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''

−	: ''ID: Yes, 'center' it is defined by IM, but if you see this example	+	: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''
−	http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''

← Older revision		Revision as of 18:25, 16 January 2009
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	Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.		Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.

−	''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''	+	: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''
		+
		+	: ''ID: Yes, 'center' it is defined by IM, but if you see this example
		+	http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''

← Older revision		Revision as of 15:41, 16 January 2009
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	===Important Note===		===Important Note===
	Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.		Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.
		+
		+	''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''

@@ Line 84: / Line 84: @@
 ** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).
 ** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.
-* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as described above.
+* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].
 ===Important Note===
 Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.