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ConceptMapper

2010-03-31T17:03:54Z

uid=jones,o=NCEAS changed this page on Wed Mar 31 10:03:54 PDT 2010:


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- ConceptMapper is a desktop tool to assist taxonomists to relate taxonomic concepts from one classification to another and to manage taxonomic concept metadata that precisely define taxonomic concepts. Database schema has been developed to hold taxonomic concept data, including scientific names, concept references, character and specimen circumscription information, parent-child relationships and third-party assertions that relate concepts between different classifications. Concept data stored in the database can be retrieved, visualized and changed through the ConceptMapper user interface. Main functions include importing , exporting, querying and viewing concept data, adding and editing relationships, concepts, references and specimens. Some other features include relationship expression validation, redo/undo support and preference settings. A help document is also developed and embedded with the tool to offer background information and usage guidance. ConceptMapper can be used by taxonomists to manage their data, especially in creating mappings across multiple classifications. It can also be used by those who need to know more about taxa in data interpretation and analysis as a convenient concept exploring tool. The ConceptMapper installation program can be downloaded from: http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/taxon/conceptmapper/conceptmapper.msi?rev=1.2&content-type=text/plain
+ ConceptMapper is a desktop tool to assist taxonomists to relate taxonomic concepts from one classification to another and to manage taxonomic concept metadata that precisely define taxonomic concepts. Database schema has been developed to hold taxonomic concept data, including scientific names, concept references, character and specimen circumscription information, parent-child relationships and third-party assertions that relate concepts between different classifications. Concept data stored in the database can be retrieved, visualized and changed through the ConceptMapper user interface. Main functions include importing , exporting, querying and viewing concept data, adding and editing relationships, concepts, references and specimens. Some other features include relationship expression validation, redo/undo support and preference settings. A help document is also developed and embedded with the tool to offer background information and usage guidance. ConceptMapper can be used by taxonomists to manage their data, especially in creating mappings across multiple classifications. It can also be used by those who need to know more about taxa in data interpretation and analysis as a convenient concept exploring tool. The ConceptMapper installation program can be downloaded from:
+
+ [https://code.ecoinformatics.org/code/seek/trunk/projects/taxon/conceptmapper/conceptmapper.msi]



Past

2009-11-23T20:38:51Z

uid=jones,o=NCEAS changed this page on Mon Nov 23 12:38:51 PST 2009:


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+ **[SEEK Postdoctoral and New Faculty Training, January 8-12,2007]



OnSiteInformaticsTraining

2009-11-23T20:38:38Z

uid=jones,o=NCEAS changed this page on Mon Nov 23 12:38:38 PST 2009:


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+ No future events are scheduled.
Removed line 13
- **[SEEK Postdoctoral and New Faculty Training, January 8-12,2007]



MenuTree

2009-05-27T21:56:12Z

uid=tao,o=NCEAS changed this page on Wed May 27 14:56:12 PDT 2009:


Removed line 53
- **[CVS Repository|CVSRepository]



SVNRepository

2009-05-27T21:54:04Z

uid=tao,o=NCEAS changed this page on Wed May 27 14:54:04 PDT 2009:


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- The [SVN web interface|https://code.ecoinformatics.org/code/] provides access to any version of the documents stored in the repository. You can browse the web interface to locate single documents of interest and download the required version. The web interface is not particularly effective when you want to use an entire module. In that case, you should use a SVN client to access the SVN repository more efficiently. Documents related to SEEK are accessible through two main SVN modules:
+ The [SVN web interface|https://code.ecoinformatics.org/code/] provides access to any version of the documents stored in the repository. You can browse the web interface to locate single documents of interest and download the required version. The web interface is not particularly effective when you want to use an entire module. In that case, you should use a SVN client to access the SVN repository more efficiently. Documents related to SEEK are accessible through three main SVN modules:



Kepler

2009-03-10T18:57:07Z

NCEAS.jones changed this page on Tue Mar 10 11:57:07 PDT 2009:


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- ** [Current release|http://kepler-project.org/Wiki.jsp?page=Downloads]
+ ** [Download the current release|http://kepler-project.org/users/downloads]



NewsAndAnnouncements2004

2008-02-11T20:41:10Z

uid=berkley,o=NCEAS changed this page on Mon Feb 11 12:41:10 PST 2008:


At line 1 added 3 lines.
+ |Oct 5, 2006|SEEK Postdoctoral and New Faculty Training scheduled on Jan 8-12, 2007 in Albuquerque, NM|
+ |Sept 14, 2006|SEEK All-Hands Meeting scheduled on Dec 10–15, 2006, in Santa Barbara, CA|
+ |July 24, 2006|Kepler 1.0.0beta2 released for testing and evaluation (download)|



WelcomeToSEEK

2008-02-11T20:39:19Z

uid=berkley,o=NCEAS changed this page on Mon Feb 11 12:39:19 PST 2008:


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- |Oct 5, 2006|[SEEK Postdoctoral and New Faculty Training|SEEK Postdoctoral and New Faculty Training, January 8-12,2007] scheduled on Jan 8-12, 2007 in Albuquerque, NM
- |Sept 14, 2006|SEEK [All-Hands Meeting|AHMDec2006] scheduled on Dec 10–15, 2006, in Santa Barbara, CA
- |July 24, 2006|[Kepler] 1.0.0beta2 released for testing and evaluation ([download|http://kepler-project.org/Wiki.jsp?page=Downloads])
+ |February 11, 2008|[Kepler 1.0.0 Release Candidate 1 Released|http://kepler-project.org/Wiki.jsp?page=Downloads]



SemanticSearchExamples

2008-01-17T19:31:37Z

uid=jones,o=NCEAS created this page on Thu Jan 17 11:31:37 PST 2008:Semantic searches have been posited to significantly improve the capabilities of scientists to locate ecological and environmental data that are relvant to their particular purposes. This page provides some example searches that would be useful to be able to express and execute in the SEEK SMS system. Current metadata searches Current metadata-driven search systems allow searches against EML to retrieve relevant documents. Such searches include simple keyword matching against the full text of the metadata document, against particular metadata fields (e.g., to find the Creator of a data set), and compound searches. The compound searches use the structure of the metadata document to create a search based on space, time, biological taxonomy, or other criteria that are provided in the metadata content. Some example searches one can conduct include: Find all data sets with the term 'soil' in the metadata Find all data sets with the term 'soil' in the abstract Find all data sets with the term 'soil' and the term 'horizon' in the abstract Find all data sets with the term 'marine' in the metadata located west of 120 degrees longitude Find all data sets with the named place 'Santa Barbara County' in the geographic description Find all data sets that list 'Abies lasiocarpa' as a covered taxon Find all data sets that were collected between 1990 and 2000 Find all data sets located west of 120 degrees longitude that were collected between 1990 and 2000 that list 'Mytilus californianus' as a covered taxon Semantic searches The above searches are good, but tend to not be particularly precise nor very complete. A search for 'soil' in the KNB produces over 3000 data sets, many of which may or may not be relevant to a study on, for example, soil chemistry. On the other hand, a search on 'soil chemistry' might only match a few data sets, because that term only occurs in a few metadata records. Instead, relevant meatdata records might include terms such as 'acidity', 'salt content', 'Nitrogen', 'Potassium', 'K', 'N', etc. A semantic search system that allowed one to recognize that 'N' and 'Nitrogen' are the same concept, and that they are both related to 'SoilChemistry' would be a huge improvement. In addition, scientists are frequently searching for data with particular measurements have been made, such as 'Density estimates for abalone' or 'Solar radiation at 1m above ground'. These searches are not possible with the current metadata-based search system, and instead require a far more semantically-aware search system. Some of the searches that would be useful include (an example dataset that should match the query is included in parentheses): Find all data sets with measurements of DissolvedCarbon concentration (knb-lter-gce.259.16) Find all data sets with measurements of WaterChemistry (knb-lter-gce.259.16, knb-lter-gce.199.7) Find all data sets of Abundance of Invertebrate organisms (knb-lter-gce.24.16) Find all data sets in the intertidal zone of the Atlantic coast of the United States (knb-lter-gce.24.16, many others) Find all data sets with LeafArea and OrganicMass measurements in Grasses (knb-lter-gce.4.8) Find all data sets with Height measurements for 'Armases cinereum' sensu Abele 1992 (knb-lter-gce.23.16) Find all data sets with Abundance measurements for crabs where sampling occurred within sampling units with a minimum size of 0.5 square meters (knb-lter-gce.23.16) Find all data sets with Temperature and Salinity measurements of Water were observed in the same Observation (knb-lter-gce.139.8) Hopefully these represent a good discussion starter on semantic searches. [...]



EcoGridAuthDesign

2008-01-16T17:53:59Z

uid=leinfelder,o=NCEAS changed this page on Wed Jan 16 09:53:59 PST 2008:


At line 10 added 3 lines.
+ The Metacat implementations of these new methods have been coded and are ready to be committed to the SEEK project. Placeholder 'implementations' have been added for SRB and Digir as well. These placeholders ignore the authentication credential parameter and call the existing service implementation methods that do not require authentication (query() and get()).
+
+



EcoGridCommunity

2008-01-14T18:24:25Z

uid=leinfelder,o=NCEAS changed this page on Mon Jan 14 10:24:25 PST 2008:


At line 8 added 1 line.
+ * [EcoGrid Authentication Design|EcoGridAuthDesign]



TaxVis

2007-07-12T16:04:40Z

uid=jones,o=NCEAS changed this page on Thu Jul 12 09:04:40 PDT 2007:


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- Download from [http://www.dcs.napier.ac.uk/~marting/workFrameSEEK.hml]
+ Download from [http://www.dcs.napier.ac.uk/~marting/workFrameSEEK.html]



SEEKToolsAndData

2007-07-12T16:02:52Z

uid=jones,o=NCEAS changed this page on Thu Jul 12 09:02:52 PDT 2007:


At line 25 added 2 lines.
+ *[TaxVis|TaxVis]
+ ** A visualization tool for exploring multiple taxonomic hierarchies.



KRSMSMarch2007

2007-05-25T02:21:08Z

uid=bowers,o=SDSC changed this page on Thu May 24 19:21:08 PDT 2007:


At line 100 added 1 line.
+ |[WO8802A|http://www.vcrlter.virginia.edu/cgi-bin/w3-msql2/data/query/datasets/show_data.html?QDATA_ID=WO8802A]|Y+|Spartina alterniflora leaf measurements, part A



KRSMSSemanticAnnotationLanguage

2007-04-16T06:03:11Z

uid=bowers,o=SDSC changed this page on Sun Apr 15 23:03:11 PDT 2007: Line 125 was replaced by line 125 - + Line 148 was replaced by line 148 - SELECT R1.x, R2.x + SELECT DISTINCT R1.x, R2.x Line 162 was replaced by line 162 - + Line 202 was replaced by line 202 - + Line 253 was replaced by line 253 - + Line 278 was replaced by line 278 - + Line 341 was replaced by line 341 - + Line 361 was replaced by line 361 - + Line 388 was replaced by line 388 - + Line 412 was replaced by line 412 - + Line 440 was replaced by line 440 - + Line 486 was replaced by line 486 - + Line 507 was replaced by line 507 - + Line 536 was replaced by line 536 - + Line 552 was replaced by line 552 - + Line 556 was replaced by line 556 - + Line 623 was replaced by line 623 - + Lines 652-653 were replaced by lines 652-653 - - +[...]