16.04.2014 BiolDiv

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==User Interface==
==User Interface==
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Casey presents the user interface as it stands now - see https://www.dropbox.com/s/4u22kyukj5srx95/Screenshot%202014-02-21%2018.24.38.png. Some points raised during the discussion:
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* Casey succeeded to make it work on her own computer.
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* Parser choice should be through a combo box, not a text box, and include the option 'NIL' for no parsing (for datasets where the authority has been split off the name proper already)
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* However, she encountered difficulties to compile it in one of the FB/SLB mirror server in UBC, Vancouver, Canada ([[http://fishbase.ca/imarine/BionymPortlet.html]]). So we can see the interface and select te option, but we cannot submit.
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* Input: offer the choice (check Dima's parser as an example, http://gni.globalnames.org/parsers/new)
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* It seems that there was a confusion about this installation on .ca: FIN used that server for testing, but the interface was never thought to be installed outside the D4Science/iMarine infrastructure. Since the beginning, the goal was to develop a portlet that would be incorporated in the Biodiversity Research VRE, to complement the two data exploration tools on species and point data.
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** enter several names by cut-and paste in a text box, each name (including authority) on a separate line
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* Casey developed the application as a tool for the infrastructure, with the technologies recommended by CNR, not as an application for FIN servers. Indeed, the first developments were made on FishBase website but it was merely for [prototyping, and develop the GSAy approach.At the beginning, the collaboration with Fabio using his environment was not planned.
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** upload a file
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* After discussion posterior to the meeting, having the interface outside would allow it to be accessible without registration in the BR VRE.
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* Output: the user should be able to define how (s)he want to see the results
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* However, Leo stressed the point that having a dedicated BiOnym VRE would make the activity and product more visible, and would not prevent to use the same portlet in the BR VRE. It could be made available without registration then? (I suppose in that case, people will have to save the result on their own computer).
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** in the interface for very short lists of names, when we can expect the results to be available fast enough to make this feasible
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* GP proposed the plan for implementation.
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** download link to be emailed later, as soon as the matching process finishes (as is done in World Ocean Database for example - check WODselect)
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** 2 phases for the application implementation>
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** in the workspace for users who have an iMarine account
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*** Create a virtual server in CNR (?) where the application coud be deployed as it is.
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* include examples of what the distances between names are, and explain what the other options are, though help links
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*** Start with one word entry, then uploading a csv file.
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* make number of matchers to be used a variable number, by adding a 'Add matcher' button, and starting out with just one; up to a maximum of five matchers?
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For the time being the interface is not functional; Casey will contact GP directly to sort out any remaining problems.
 
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==Article==
 
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Nicolas started on the introduction, and will incorporate his bits in the Google document soon (work was done off-line). Nicolas and Edward to agree on who will write what - will discuss during a one-on-one skype call on Monday.
 
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We have to decide how far we want to go with BiOnym now, in terms of the complexity of the name strings we want the system to be able to handle. The bottleneck is mainly in the parser. The 'Simple' parser now only looks for uninomina (genera or above) and species. GNI parser is more sophisticated, but is very sensitive to formatting errors/errors in capitalisation. Edward and Nicolas will explore GNI parser further, also produce pseudo-code or another structured explanation on how to read and interpret the results from the GNI parser.
 
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For names including more than just a simple specific epithet, we can leave all the epithets in one string (i.e. all the nomenclatural 'atoms' following the genus name, but before the authority). This is done by FishBase.
 
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For hybrids, in principle we should parse the name string, and replace it with two scientific names, one for each of the 'parents' of the hybrid: our TAFs don't list hybrids, but in principle they do list each of the parents separately. Dealing with this situation for BiOnym is probably going to be too complicated at this point. For the time being, if we find out that we're dealing with a hybrid (e.g. because it's flagged as such by the GNI parser, or because we've detected a 'x' between two spaces), we should not even try and match (we'd only increase our false positives).
 
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==Validation==
 
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Anton announces that the validation of the BiOnym activities has started, as this is a deliverable for iMarine due pretty soon. Anton and Edward are working on this together.
 
=Next meetings=
=Next meetings=
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Monday 24 February, 11:00 am European time for Nicolas and Edward
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Thursday 17 April 2014, 11:00 am European time for discussion on the paper.
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Thursday 27 February, 11:00 am for the group
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Revision as of 08:06, 21 April 2014

Meeting 16 April 2014, 11:00 am

Google Hangout

Present: Fabio, Nicolas, Casey, Edward, Lino, Leo, Anton (at the beginning)


Contents

Edward's report

To be discussed with Lino and Anton on Thursday 17 Aapril 2014.

BiOnym paper

To be discussed on Thursday 17 Aapril 2014.

Notes

User Interface

  • Casey succeeded to make it work on her own computer.
  • However, she encountered difficulties to compile it in one of the FB/SLB mirror server in UBC, Vancouver, Canada ([[1]]). So we can see the interface and select te option, but we cannot submit.
  • It seems that there was a confusion about this installation on .ca: FIN used that server for testing, but the interface was never thought to be installed outside the D4Science/iMarine infrastructure. Since the beginning, the goal was to develop a portlet that would be incorporated in the Biodiversity Research VRE, to complement the two data exploration tools on species and point data.
  • Casey developed the application as a tool for the infrastructure, with the technologies recommended by CNR, not as an application for FIN servers. Indeed, the first developments were made on FishBase website but it was merely for [prototyping, and develop the GSAy approach.At the beginning, the collaboration with Fabio using his environment was not planned.
  • After discussion posterior to the meeting, having the interface outside would allow it to be accessible without registration in the BR VRE.
  • However, Leo stressed the point that having a dedicated BiOnym VRE would make the activity and product more visible, and would not prevent to use the same portlet in the BR VRE. It could be made available without registration then? (I suppose in that case, people will have to save the result on their own computer).
  • GP proposed the plan for implementation.
    • 2 phases for the application implementation>
      • Create a virtual server in CNR (?) where the application coud be deployed as it is.
      • Start with one word entry, then uploading a csv file.



Next meetings

Thursday 17 April 2014, 11:00 am European time for discussion on the paper.

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