16:03:01 <RRSAgent> RRSAgent has joined #BioRDF
16:03:01 <RRSAgent> logging to http://www.w3.org/2007/11/26-BioRDF-irc
16:03:07 <ericP> Zakim, this is BioRDF
16:03:07 <Zakim> ok, ericP; that matches SW_HCLS(BioRDF)11:00AM
16:03:20 <Susie> SenseLab URL - http://senselab.med.yale.edu/SenseLab Public Snapshot 20071119.zip
16:03:22 <mscottm> mscottm has joined #biordf
16:03:36 <Zakim> + +20416aacc
16:03:46 <Zakim> +Alan_Ruttenberg
16:05:15 <ericP> Zakim, please dial ericP-415
16:05:21 <Zakim> ok, ericP; the call is being made
16:05:23 <Zakim> +EricP.a
16:05:43 <ericP> scribe: ericP
16:06:15 <Susie> SenseLab Conversion into Access tables - Luis Marenco (zip file) 
16:07:13 <ericP> Topic: SenseLab Conversion
16:07:52 <Susie> SenseLab URL - http://senselab.med.yale.edu/SenseLab Public Snapshot 20071119.zip
16:08:13 <ericP> -> http://senselab.med.yale.edu/ SenseLab Homepage
16:08:39 <ericP> -> http://senselab.med.yale.edu/site/dsArch/?lb=tree  SenseLab Archicture Page
16:09:11 <Susie> Agenda 1 - SenseLab Conversion into Access tables - Luis Marenco (zip file) 
16:09:23 <Susie> Agenda 2 - SenseLab Conversion Documentation - Matthias 
16:09:34 <mscottm> yes
16:09:38 <Susie> Agenda 3 - Knowledgebase extensions - Alan 
16:09:50 <Susie> Agenda 4 - KB Documentation - Alan 
16:09:55 <ericP> -> http://senselab.med.yale.edu/site/dsarch/images/visio-eavcr_physical_schema_021205.png SenseLab ER diagram
16:10:48 <ericP> Luis: pink boxes, internal tables, are there now
16:11:31 <ericP> ... blue box also done
16:12:28 <ericP> ... senselab_db table corresponds to this diagram
16:12:53 <ericP> ... generally, remove the "senselab_"
16:13:47 <ericP> ... re senselab_classes (called "classes" in the ER): class_db_owner tells you to which db that class belongs
16:14:18 <ericP> ... class_type tells you the type of class
16:14:23 <ericP> ... .. E for entity
16:14:27 <ericP> ... .. A for association
16:14:45 <ericP> ... A is just a bridge class
16:14:57 <ericP> alanr: example?
16:15:12 <ericP> luis: later on
16:15:26 <ericP> ... ER dump is from Oracle
16:16:11 <ericP> ... will add links to access database
16:16:41 <ericP> ... attributes class includes the attributes defined for each class
16:17:09 <Zakim> -Alan_Ruttenberg
16:17:29 <Zakim> -??P13
16:17:39 <Zakim> +[MIT-G346]
16:18:07 <Zakim> +??P4
16:18:24 <ericP> luis: attribute caption is a human-readable name
16:18:29 <alanr> alanr has joined #biordf
16:18:31 <ericP> ... attribute description
16:18:38 <ericP> ... attribute datatype:
16:18:51 <ericP> ... .. S string -- up to 255 characters
16:19:04 <ericP> ... .. N numeric -- any real/integer/whatever
16:19:16 <ericP> ... . M memo -- up to two G
16:19:34 <ericP> ... .. can have as many memo fields as you want for a particular table
16:19:41 <ericP> ... .. D datetime -- short or long
16:19:54 <ericP> ... .. Y binary -- binary string stored in the DB
16:21:16 <ericP> ericP: both M memo and Y binary are BLOBs?
16:21:26 <ericP> luis: depends on impl
16:21:39 <mscottm> mscottm has joined #biordf
16:21:39 <ericP> susie: you are using Oracle 10G?
16:21:43 <ericP> luis: yes
16:22:04 <ericP> alanr: distinction between memo and binary?
16:22:16 <ericP> luis: [@@ missed]
16:22:30 <ericP> kei: you lost binary fields?
16:22:44 <ericP> alanr: lost them in the MySQL, but preserved in the XML
16:23:27 <ericP> ... if you do a separate query fro the memofields and save them as, say, Base64...
16:24:01 <Zakim> -[MIT-G346]
16:24:08 <ericP> susie: careful, LONG is likely to be lost from the Oracle support
16:24:17 <Zakim> +[MIT-G346]
16:24:20 <ericP> luis: have lots of legacy code
16:24:31 <alanr> zakim, [MIT-G346] is me
16:24:31 <Zakim> +alanr; got it
16:24:59 <ericP> luis: I integer
16:25:07 <ericP> ... C object reference
16:25:18 <ericP> ... .. H for hierarchy
16:26:09 <ericP> ... attributes can have 1:1 or 1:many mapping
16:27:01 <alanr> "DATATYPE"	"NAME"	"DESCRIPTION"	"XML_DATATYPE"	"TABLE_NAME"
16:27:02 <alanr> "C"	"Object/Ref"	"Object reference (pointer)"	"xs:long"	"EAV_OBJECTS"
16:27:03 <ericP> ... hierarchy is a variation of C, but used for references to the same class
16:27:04 <alanr> "D"	"Datetime"	"Datetime"	"xs:dateTime"	"EAV_DATE"
16:27:05 <alanr> "F"	"Formula(only)"	"Formula (only)"	"xs:anyType"	"EAV_STRING"
16:27:07 <alanr> "H"	"Hierarchy(p)"	"Hierarchy (to parent object)"	"xs:long"	"EAV_OBJECTS"
16:27:08 <alanr> "I"	"Integer"	"Integer"	"xs:long"	"EAV_INT"
16:27:10 <alanr> "M"	"Memo"	"Free Text"	"xs:string"	"EAV_MEMO"
16:27:11 <alanr> "R"	"Real"	"Floating point values"	"xs:double"	"EAV_REAL"
16:27:13 <alanr> "S"	"String"	"String"	"xs:string"	"EAV_STRING"
16:27:14 <alanr> "V"	"Object/Value"	"Object/Value (elaborate)"	"xs:long"	"EAV_OBJECTS"
16:27:16 <alanr> "Y"	"Binary"	"Any binary string (files)"	"xs:base64Binary"	"EAV_BINARY"
16:27:17 <alanr> "B"	"Boolean"	"Boolean"	"xs:boolean"	"EAV_INT"
16:27:52 <alanr> hierarchy H can omit the class compared to C. Same class as referrer
16:28:15 <ericP> luis: examing objects table:
16:28:22 <alanr> EAV:OBJECT - Headers: "OBJECT_CLASS"	"OBJECT_ID"	"OBJECT_NAME"	"OBJECT_DESCRIPTION"	"CREATED"	"MODIFIED_BY"	"PRIVATE"	"OWNER"	"ASSOCIATION"	"VER_NUMBER"	"VER_DATE"
16:28:59 <ericP> ... you only get the entries where OBJECT.PRIVATE=FALSE
16:29:03 <alanr> s/EAV:OBJECT/SENSELAB_OBJECT/
16:29:47 <ericP> ... VALUEs tables:
16:29:59 <ericP> ... .. EAV_STRING table
16:30:04 <Zakim> -Karen_Skinner
16:30:10 <alanr> SENSELAB_EAV_STRING: "OBJECT_ID"	"ATTRIBUTE_ID"	"VALUE_"
16:30:28 <ericP> ... .. real, date, memos...
16:30:33 <alanr> e.g. "4085"	"158"	"Neuroscience"
16:30:52 <ericP> ... serial number allows ordering of 1:many references
16:32:18 <ericP> ... example: a serial number will tell you in which order you wish to see the receptors of a neuron
16:32:19 <alanr> SENSELAB_EAV_OBJECT, serial number - when there are multiple objects, how to order them. 
16:32:40 <alanr> For display onyl
16:33:36 <alanr> SENSELAB_SEMRELA : "ID"	"NAME"	"INVERSE"	"UMLS_ID"	"ABR"
16:33:54 <ericP> luis: semantic table start with semantic_
16:34:05 <alanr> "0"	"(none) Top"			
16:34:07 <alanr> "1"	"is a"		"T186"	"IS"
16:34:08 <alanr> "2"	"is of type"			
16:34:10 <alanr> "3"	"is named"			
16:34:11 <alanr> "4"	"is also named"			
16:34:13 <alanr> "5"	"described in Genbank as"			
16:34:14 <alanr> "6"	"whose gene is on"			
16:34:16 <alanr> "7"	"information obtained from"			
16:34:17 <alanr> ...
16:34:44 <ericP> s/semantic_/senselab_/
16:35:23 <alanr> "20"	"Biological Properties"			
16:35:31 <alanr> "19"	"is expressed in"			
16:35:39 <ericP> alanr: "biological property" is a parent of "expressed in"
16:36:07 <alanr> SENSELAB_SEMRELA_HIERARCHY: 
16:36:09 <alanr> "PARENT_ID"	"CHILD_ID"	"STN_RTN"
16:36:10 <alanr> ....
16:36:12 <alanr> "20"	"19"	
16:36:13 <alanr> ....
16:36:19 <ericP> luis: we have XML files with <semantics/><schema/><data/>
16:36:32 <ericP> ... wanted this readable in the future
16:36:56 <ericP> ... semantic relationship attributes can connect two attributes
16:37:03 <alanr> SEMRELT: "ID"	"NAME"	"UMLS_NAME"	"UMLS_ID"
16:37:18 <ericP> ... semantic relationship types: modeled the same as the UMLS
16:37:27 <alanr> "ID"	"NAME"	"UMLS_NAME"	"UMLS_ID"
16:37:29 <alanr> "1"	"Class qualifies Attribute"	"1st concept qualifies 2nd"	"QB"
16:37:30 <alanr> "2"	"Class is parent of Attribute"	"1st is parent of 2nd"	"CHD"
16:37:32 <alanr> "3"	"Attribute has relationship other than synonomous"	"2nd concept has relationship other than synonomous"	"RO"
16:37:33 <alanr> "4"	"Attribute is broader than Class"	"2nd concept is broader than 1st"	"RB"
16:37:35 <alanr> "5"	"Attribute is narrower than Class"	"2nd concept is narrower than 1st"	"RN"
16:37:36 <alanr> "6"	"Attribute qualifies Class"	"2nd concept qualifies 1st"	"AQ"
16:37:38 <alanr> "7"	"Attribute is parent of Class"	"2nd is parent of 1st"	"PAR"
16:37:39 <alanr> "8"	"sibling relationship"	"sibling relationship"	"SIB"
16:37:41 <alanr> "9"	"Similar or alike concepts"	"Similar or alike concepts"	"RL"
16:37:48 <ericP> ... semantic type attribute: mammal, human, ...
16:38:12 <ericP> ... is many to many
16:38:23 <ericP> ... dictionary table:
16:38:37 <alanr> DICTIONARY: 
16:38:38 <alanr> "ELEM_TYPE"	"ELEM_ID"	"UMLS_ID"	"UMLS_NAME"
16:38:40 <alanr> "A"	"3"	"C0441469"	
16:38:41 <alanr> "O"	"3542"	"C0030708"	
16:38:43 <alanr> "C"	"19"	"C0026336"	
16:38:44 <alanr> ...
16:38:45 <ericP> ... .. type: object, attribute, class
16:39:59 <alanr> key into corresponding table
16:40:19 <ericP> ... attributes ID points to PK of object, attribte or class
16:40:40 <ericP> ... no one used universal ID
16:41:37 <ericP> alanr: will be simpler in RDF 'cause these will be URIs
16:42:11 <ericP> luis: we may have URIs for these [objects, attributes, classes]
16:43:13 <ericP> -> http://senselab.med.yale.edu/site/a_raf/controls/treeFrame.asp?fs=/site/dsArch/wAdmTree.asp whatever
16:43:48 <ericP> [expanding Schema Manager/Databases/neurondb]
16:44:17 <alanr> http://senselab.med.yale.edu/site/dbMeta/eavMD_Classes.asp?cl=18
16:47:34 <alanr> http://senselab.med.yale.edu/site/dbMeta/eavMD_Classes.asp?cl=25
16:48:34 <ericP> -> http://senselab.med.yale.edu/site/dbMeta/eavMD_Attributes.asp?cl=25 attributes for NuuronDB ncr
16:49:01 <alanr> property_present 0 = negation
16:50:34 <ericP> luis: in http://senselab.med.yale.edu/site/dbMeta/eavMD_Classes.asp?cl=25 , Extensds Class should include Neuron
16:50:49 <alanr> association class = extra properties of a class. For sharing among several classes. Kind of a mixin?
16:51:44 <ericP> Susie: Luis, thanks for this tour
16:51:45 <matthiassamwald> http://esw.w3.org/topic/HCLS/Senselab_Conversion?action=show
16:51:59 <ericP> Topic: SenseLab Conversion Documentation
16:52:31 <ericP> matthiassamwald: recently expanded Experiences with the conversion of SenseLab databases to RDF/OWL
16:52:43 <ericP> ... added links to source files
16:52:59 <ericP> ... and liks to the ontology files
16:53:05 <ericP> ... still missing:
16:53:30 <ericP> ... .. some snapshots of the dev process
16:53:56 <ericP> ... .. last automated RDF conversion
16:54:31 <ericP> ... in which form coud this description become and official HCLS document?
16:54:44 <alanr> IG Note
16:55:05 <alanr> Magic HTML format
16:55:13 <mscottm> http://www.w3.org/2005/07/pubrules
16:55:44 <ericP> susie: some W3C docs hilight the format for publishing IG Notes (and others)
16:56:05 <ericP> alanr: mscottm will own the HTML template
16:57:44 <mscottm> http://www.w3.org/Guide/transitions
16:58:13 <ericP> -> http://www.w3.org/Guide/transitions Organize a Recommendation Track Transition
16:58:16 <matthiassamwald> http://esw.w3.org/topic/HCLS/Semantic_Web_Step_By_Step
16:58:39 <ericP> -> http://esw.w3.org/topic/HCLS/Semantic_Web_Step_By_Step Step by step: Creating interoperable Semantic Web resources
16:59:39 <ericP> matthiassamwald: how to phrase tutorial
16:59:52 <ericP> alanr: seems safer to say "here's how we did it"
17:00:19 <ericP> matthiassamwald: may be worth saying "this is the best way"
17:01:18 <ericP> next meeting: next week
17:01:19 <Zakim> -alanr
17:01:27 <Zakim> - +1.317.277.aaaa
17:01:36 <Zakim> -Don_Doherty
17:02:06 <ericP> susie: will discuss documentation on the next call
17:02:16 <ericP> RRSAgent, please draft minute
17:02:16 <RRSAgent> I'm logging. I don't understand 'please draft minute', ericP.  Try /msg RRSAgent help
17:02:20 <Zakim> -??P4
17:02:29 <ericP> Zakim, please draft minute
17:02:29 <Zakim> I don't understand 'please draft minute', ericP
17:02:41 <ericP> Zakim, please draft minutes
17:02:41 <Zakim> I don't understand 'please draft minutes', ericP
17:02:44 <ericP> RRSAgent, please draft minutes
17:02:44 <RRSAgent> I have made the request to generate http://www.w3.org/2007/11/26-BioRDF-minutes.html ericP
17:04:26 <ericP> <h3><a name="foo">5. Foo</a></h3>
17:04:34 <ericP> <h3 id="foo">5. Foo<//h3>
17:04:45 <matthiassamwald> exit
17:04:51 <matthiassamwald> (oops)
17:20:31 <Zakim> - +1.203.737.aabb
17:21:06 <ericP>  -> http://www.w3.org/2001/sw/DataAccess/rq23/rq25  SPARQL
17:21:19 <ericP> http://www.w3.org/2001/sw/DataAccess/rq23/rq25,validate
17:21:35 <ericP> http://www.w3.org/2001/sw/DataAccess/rq23/rq25,checklink
17:24:35 <mscottm> pcl-cvs
17:26:19 <mscottm> nxml-mode
17:30:41 <mscottm> ssh-keygen
18:07:20 <Zakim> - +20416aacc
18:07:31 <Zakim> -EricP.a
18:07:33 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
18:07:34 <Zakim> Attendees were Karen_Skinner, +1.317.277.aaaa, Don_Doherty, +1.203.737.aabb, +20416aacc, Alan_Ruttenberg, EricP.a, alanr
18:08:49 <mscottm> zakim, +20416aacc is me
18:08:49 <Zakim> sorry, mscottm, I do not recognize a party named '+20416aacc'
18:08:59 <mscottm> was me
18:45:32 <Susie> rrsagent, make logs world-visible
20:24:33 <Zakim> Zakim has left #BioRDF