Difference between revisions of "13.06.2014 BiolDiv"
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(Created page with "'''Meeting Friday 13 June 2014''' Present: Fabio (until 10:40), GP, Nicolas, Casey, Edward. ==Notes== ===WPS=== * OGC protocol: specifications for processing. Used by Terradue...") |
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* Developed for BiOnym asking to Taverna staff to check for coherence. Some adjustment were necessary but works now for Taverna workflow. | * Developed for BiOnym asking to Taverna staff to check for coherence. Some adjustment were necessary but works now for Taverna workflow. | ||
* To be used by FishBase in August 2014 version. To be compared with the call of API in the Statistical Manager. | * To be used by FishBase in August 2014 version. To be compared with the call of API in the Statistical Manager. | ||
| − | * Catalogue of WPS services available in the infrastructure: [[http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities]http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities] which is read by WPS indexing engines. | + | * Catalogue of WPS services available in the infrastructure: [[http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities]http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities] which is read by WPS indexing engines. More information on the syntax in http://wps.statistical.d4science.org/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&Identifier=org.gcube.dataanalysis.statistical_manager_wps_algorithms.generated.Bionym_local |
* Index BiOnym in MyExperiment for Taverna users after one week to let Anton, Edward and Nicolas checking the political issues to be indexed in MyExperiment. | * Index BiOnym in MyExperiment for Taverna users after one week to let Anton, Edward and Nicolas checking the political issues to be indexed in MyExperiment. | ||
| − | * Ask Tony Rees, Yde de Jong, GBIF people, more? to check the interface (Nicolas, Edward). | + | * Ask Tony Rees, Yde de Jong, GBIF people, more? to check the interface (Nicolas, Edward; 'more' could include Dima, Rod Page, BioVel). |
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* Discussion on most likely journals (expensive options like PLosOne discarded): | * Discussion on most likely journals (expensive options like PLosOne discarded): | ||
** Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals). | ** Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals). | ||
| − | ** | + | *** More spin-off papers are possible targeted at specific sub-communities; e.g. a paper demonstrating the use of BiOnym in Ecology/Biogeography for Ecological Informatics (http://www.journals.elsevier.com/ecological-informatics/) or Ecography (http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291600-0587); or a paper demonstrating the use of BiOnym for BioInformatics/sequence analysis |
| + | ** Informatics paper: not clear what such a paper would describe apart from the GCube infrastructure; needs some thinking. | ||
Latest revision as of 14:55, 13 June 2014
Meeting Friday 13 June 2014
Present: Fabio (until 10:40), GP, Nicolas, Casey, Edward.
Notes
WPS
- OGC protocol: specifications for processing. Used by Terradue and IRD.
- xml-based interface: accept REST requests. Output in xml format following xsd.
- Developed for BiOnym asking to Taverna staff to check for coherence. Some adjustment were necessary but works now for Taverna workflow.
- To be used by FishBase in August 2014 version. To be compared with the call of API in the Statistical Manager.
- Catalogue of WPS services available in the infrastructure: [[1]http://wps.statistical.d4science.org/wps/WebProcessingService?service=WPS&Request=GetCapabilities] which is read by WPS indexing engines. More information on the syntax in http://wps.statistical.d4science.org/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&Identifier=org.gcube.dataanalysis.statistical_manager_wps_algorithms.generated.Bionym_local
- Index BiOnym in MyExperiment for Taverna users after one week to let Anton, Edward and Nicolas checking the political issues to be indexed in MyExperiment.
- Ask Tony Rees, Yde de Jong, GBIF people, more? to check the interface (Nicolas, Edward; 'more' could include Dima, Rod Page, BioVel).
BiOnym Interface
- Ticket sent by Fabio.
- Casey replied Friday morning and uploaded the corrections as version 5 (another subversion to be sent by Casey after integration of 2 matchers by default, see below).
- Just an issue on double quotes around scientific names to be fixed.
- Decision on matchers by default: GSAy first, TriGrams second. Let's start with that default and test.
- Computing capacity for BiOnym: 16 synchronous requests are possible. Should be enough even if there are heavy requests (big files, several TAFs).
Paper
- Integration of latest corrections.
- Submission to day.
- Few days for light review by CNR publishers and then published.
- Discussion on most likely journals (expensive options like PLosOne discarded):
- Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals).
- More spin-off papers are possible targeted at specific sub-communities; e.g. a paper demonstrating the use of BiOnym in Ecology/Biogeography for Ecological Informatics (http://www.journals.elsevier.com/ecological-informatics/) or Ecography (http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291600-0587); or a paper demonstrating the use of BiOnym for BioInformatics/sequence analysis
- Informatics paper: not clear what such a paper would describe apart from the GCube infrastructure; needs some thinking.
- Biological paper: target Biodiversity Informatics (Nicolas to check BioMed journals).
Next meeting
Friday 20th June 2014, 10 am, changed from Thursday due to Holiday (again!) in the Philippines on 19th.
