Science Environment for Ecological Knowledge
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Science Environment for Ecological Knowledge









 

 

 



KR Meeting July 06

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- Hotel: [Marina Beach Motel|http://www.marinabeachmotel.com/Golf_Frameset.html\\
+ Hotel: [Marina Beach Motel|http://www.marinabeachmotel.com/index2.htm]\\
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- From the airport, you may book SuperRide Airport Shuttle (805-683-9636) or take a cab. A cab is $20-$25 one way.
+ From the airport, you may book SuperRide Airport Shuttle (805-683-9636) or take a cab. A cab is $20-$25 one way (I think). If you have any problems, call Josh on 805-452-7017.
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- !!! Meeting Notes
+ !!! Schedule
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+ !! Sunday, July 30th
+ * Arrivals
+
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- !!! Links
+ !!! Agenda
+ ! Priority levels: (''1'') High, (''2'') Medium, (''3'') Low
+
+ !! Wednesday TODO:
+ * Discuss annotation GUI
+ ** Kepler or Morpho?
+ ** Should we move forward creating Kepler actor for "sensible" summarisation without annotation GUI
+
+ !! OBOE (''1'')
+ * Finalize structure so can begin publication, process, and extension processes [PRETTY MUCH DONE]
+ ** TREE proposal
+ ** URL
+ ** OBOE guide
+ * Focus will be directed mainly at the Measurement Standard/Units region of the ontology [DONE]
+ ** We need to come to a concensus about how we are going to represent units for quantitative and qualitative/continuous and discrete unit types [DONE]
+ * Add copyright/licence (GPL)/restrictions in to OWL ontologies metadata field; enter version IDs.
+ ** Licence file goes in folder -- get from Morpho
+ ** Copy right statement in OWL file -- see Morpho documents (GPL)
+ ** CVS IDs
+
+ __Action items:__\\
+ Steps: 1. Implement changes in OWL; 2. Upload to URL; 3. Work on illustraive examples; 4. Draft guide; 5. Submit TREE porposal; 6. Decide name for ontology; \\
+ By who: Josh, with help from Shawn\\
+ By when: End of August\\
+
+ !! Extension ontologies (''1'')
+ * Produce a draft convention for engineering extension ontologies
+ ** Extension points: Entity, Characteristic, Measurement Standard, and Context
+ ** Evaluation process
+ * Producing foundational controlled vocabularies
+ ** Methods (e.g., text parsing)
+ ** Browsing (e.g., online thesaurus-type browsing)
+ * Evaluation and filling-in of foundational controlled vocabulary
+ ** E.g., public wikipedia-like interface for ecologists to add/edit/debate ecological concepts and relationships
+ __Action items:__\\
+ Steps: 1. Produce SEEK set of high-level extesion ontologies, primarily for illustrative purposes; 2. Write set of instructions/rules for creating extension ontologies for other groups/initiatives.\\
+ By who: Josh\\
+ By when: End of September\\
+
+ !! Representing annotations (''1'')
+ * Discussion of ways to store OBOE data annotations
+ ** EML extension/new module
+ ** Short term versus long term considerations
+ __Action items:__\\
+ Steps: 1. Decide on syntax/language for annotation; 2. Develop GUI for annotation; 3. Decide where/how annotation syntax will be saved\\
+ By who: Shawn, with help from Josh\\
+ By when: End of September\\
+
+ !! Versioning and backward compatibility issues (''2'')
+ * E.g., OBOE's constant structural changes have made it hard to create extension ontologies
+ __Action items:__\\
+ Steps: ...\\
+ By who: ...\\
+ By when: ...\\
+
+ !! Data summarization (''2'')
+ * Demostration of summarization capabilities enabled by OBOE
+ __Action items:__\\
+ Steps: 1. Create basic summarization actor in kepler that reads annotation and ...\\
+ By who: Josh\\
+ By when: End of September\\
+
+ !! Operation over observations and measurements (''2'')
+ * Demonstration of compatibility and conversion using OBOE
+ * Flush out all function necessary for simple data merge
+ __Action items:__\\
+ Steps: 1. \\
+ By who: ...\\
+ By when: ...\\
+
+ !! ENM issues (''3'')
+ * Examine document provided by Deana
+ *[ENM Document | http://rupert.msi.ucsb.edu/~madin/ENMKRneeds.doc] (DOC)
+ __Action items:__\\
+ Steps: ...\\
+ By who: ...\\
+ By when: ...\\
+
+ !!! Links and Ontologies
+
+ *[SEEK WebPage | http://seek.ecoinformatics.org/]
+ *[NCEAS WebPage | http://www.nceas.ucsb.edu/]
+
+ !OBOE
+
+ *[OBOE and other ontologies in cvs | http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/kr-sms/kr/ontologies/OBOE/] (OWL format)
+ *[Current incarnation | http://rupert.msi.ucsb.edu/~madin/OBOE_master_3.pdf] (PDF)
+
+ !GO (the Gene Ontology)
+
+ *[GO WebPage | http://www.geneontology.org/]
+ *[GO daily terms (OWL format) | http://archive.godatabase.org/latest-termdb/go_daily-termdb.owl.gz]
+
+ !DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering)
+
+ *[DOLCE WebPage | http://www.loa-cnr.it/DOLCE.html]
+ *[DOLCE lite (OWL format) | http://www.loa-cnr.it/ontologies/DLP3971.zip]
+
+ !SWEET (Semantic Web for Earth and Environmental Terminology)
+
+ *[SWEET ontologies (OWL format) | http://sweet.jpl.nasa.gov/ontology]
+
+ !SUO (Standard Upper Ontology)
+
+ *[SUO WebPage | http://suo.ieee.org/]
+ *[SUO Framework | http://suo.ieee.org/IFF/]
+
+ !FMA (Foundational Model of Anatomy)
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- * UCD (Uniform Content Descriptors) [http://vizier.u-strasbg.fr/doc/UCD/inVizieR.htx]
+ *[FMA home | http://sig.biostr.washington.edu/projects/fm/index.html]
+ *[Foundational Model Explorer | http://fme.biostr.washington.edu:8089/FME/index.html] is a web-based tool for browsing the ontology
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+ !UCD (Uniform Content Descriptors)
+ *[http://vizier.u-strasbg.fr/doc/UCD/inVizieR.htx]
+
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