Difference between revisions of "29.08.2013 BioDiv"
From D4Science Wiki
(Created page with "'''iMarine Biodiversity Cluster''' Next Skype meetings: Friday 30th August 2013: # Nicolas, Casey 10:00 Rome time. # Edward, Nicolas 14:00 Rome time '''Notes''' from the Skype ...") |
|||
| Line 10: | Line 10: | ||
* Nicolas to go to Oostende on Friday 6th Sept. | * Nicolas to go to Oostende on Friday 6th Sept. | ||
| − | From there the points discussed are the same as in the to do list Edward document: iMarine_to_do_Edward.docx | + | From there the points discussed are the same as in the to do list Edward document: iMarine_to_do_Edward.docx, [[http://goo.gl/T9w3nC]] |
'''Master plan''' | '''Master plan''' | ||
| − | * Update master document: for the review. | + | * Update master document/biodiversity mapping: in time for the review [[http://goo.gl/IYspDn]]. |
| − | * Wiki on the biodiversity cluster page, the internal technical and management document. But also complete the wiki page for the product | + | * Wiki on the biodiversity cluster page, the internal technical and management document. But also complete the wiki page for the product BiolCube for external communication (http://wiki.i-marine.eu/index.php/Catalogue:Applications#BiolCube): both for the review, Nicolas and Edward to review. |
'''Taxonomy''' | '''Taxonomy''' | ||
| − | * Document updated. | + | * Document describing report format of comparing different methods of name matching is updated [[http://goo.gl/09yGHN]]. |
| − | * Dima not ready. Most probably ready Friday 30th Aug. | + | * Dima not ready with next version of parser. Most probably ready Friday 30th Aug. |
* To check with Casey: Nicolas on Friday 30th by Skype. | * To check with Casey: Nicolas on Friday 30th by Skype. | ||
* Test datasets sent by Nicolas to be clarified. To be discussed on Friday 30th by Skype at 2pm Nicolas/Edward by Skype. | * Test datasets sent by Nicolas to be clarified. To be discussed on Friday 30th by Skype at 2pm Nicolas/Edward by Skype. | ||
| Line 25: | Line 25: | ||
* Rule frame work to be resumed. | * Rule frame work to be resumed. | ||
* Establish a unique workflow for taxon name match among all functionalities with series (and possibly parallel workflow (Friday 6th). Contact Tony for discussion about the new version of TaxaMatach and IRMNG (Edward to contact Tony to get an appointment with him on Friday 6 Sept.). | * Establish a unique workflow for taxon name match among all functionalities with series (and possibly parallel workflow (Friday 6th). Contact Tony for discussion about the new version of TaxaMatach and IRMNG (Edward to contact Tony to get an appointment with him on Friday 6 Sept.). | ||
| − | * Establish the community list with whom we want to share the work (e.g., GBIF, GNA) for a further discussion, after the one with Tony. Describe the users of these tools, and how to spread it into the community in wiki. Be sure that tools can be used by external users at some point. | + | * Establish the community list with whom we want to share the work (e.g., GBIF, GNA) for a further discussion, after the one with Tony. Describe the users of these tools, and how to spread it into the community in wiki. Be sure that tools can be used by external users at some point. Contact Yde to check whether we can present our taxon name matching work in a poster presentation during the TDWG meeting in October, in Firenze. |
* Name reconciliation workflow: resume the work Friday 6th, not needed for the review. | * Name reconciliation workflow: resume the work Friday 6th, not needed for the review. | ||
'''Environmental variables''' | '''Environmental variables''' | ||
| − | * Edward to re-circulate the document ( | + | * Edward to re-circulate the document on priority layers of environmental parameters to be used for Species Distribution modelling (Lino, GP, Nicolas, Fabrice, Julien). |
* Work in progress on Tuna and high seas. | * Work in progress on Tuna and high seas. | ||
| − | * Bio-ORACLE | + | * Bio-ORACLE deals only with surface data, and is already gridded/summarised; so it is not the type of data we were looking for. Need for looking in which cases it can be used, and look for complement in NODC (see below). |
* Bio-ORACLE works in R. Further niche modeling options to be explored by Edward. | * Bio-ORACLE works in R. Further niche modeling options to be explored by Edward. | ||
| − | * Edward to get in touch with Fabrice (linked with first point). | + | * Edward to get in touch with Fabrice (linked with first point), and explore functionality of data extraction created by TerraDue. |
| − | * Edward to | + | * Edward to organise conference call with NODC/WDC to try and learn from their experiences in creating the World Ocean Atlas out of the World Ocean Database. Implementation by CNR and/or TerraDue, to be discussed. Nicolas to check with CRIA if they are still interested in the validation part. |
'''Identifying outliers in environmental space''' | '''Identifying outliers in environmental space''' | ||
| − | |||
* Edward explored DBScan vs LOF with help of GP. In conclusion LOF is preferred, and a report is being prepared. Issue on GP's availability to check with CNR for further work. | * Edward explored DBScan vs LOF with help of GP. In conclusion LOF is preferred, and a report is being prepared. Issue on GP's availability to check with CNR for further work. | ||
* Contact CRIA next week (Nicolas alone, and on Friday 6th with Edward). | * Contact CRIA next week (Nicolas alone, and on Friday 6th with Edward). | ||
| Line 52: | Line 51: | ||
'''Guidelines, Policies and Training Material''' | '''Guidelines, Policies and Training Material''' | ||
* To be done later. | * To be done later. | ||
| − | * Use the R vignette style to produce such documents. | + | * Use the R vignette style to produce such documents. Species Distribution Modelling vignette by Hijmans and Elith could serve as an example ([http://cran.r-project.org/web/packages/dismo/vignettes/sdm.pdf sdm.pdf on CRAN]) |
'''Other''' | '''Other''' | ||
* Try to meet with GP on Sept. 10th. | * Try to meet with GP on Sept. 10th. | ||
Latest revision as of 10:38, 30 August 2013
iMarine Biodiversity Cluster
Next Skype meetings: Friday 30th August 2013:
- Nicolas, Casey 10:00 Rome time.
- Edward, Nicolas 14:00 Rome time
Notes from the Skype meeting held on Thursday 29th August 2013 Anton, Edward, Nicolas. 14:00-15:30 Rome time
- Nicolas to go to Oostende on Friday 6th Sept.
From there the points discussed are the same as in the to do list Edward document: iMarine_to_do_Edward.docx, [[1]]
Master plan
- Update master document/biodiversity mapping: in time for the review [[2]].
- Wiki on the biodiversity cluster page, the internal technical and management document. But also complete the wiki page for the product BiolCube for external communication (http://wiki.i-marine.eu/index.php/Catalogue:Applications#BiolCube): both for the review, Nicolas and Edward to review.
Taxonomy
- Document describing report format of comparing different methods of name matching is updated [[3]].
- Dima not ready with next version of parser. Most probably ready Friday 30th Aug.
- To check with Casey: Nicolas on Friday 30th by Skype.
- Test datasets sent by Nicolas to be clarified. To be discussed on Friday 30th by Skype at 2pm Nicolas/Edward by Skype.
- Bionym document in constant in working progress: can be provided as such if needed for the review.
- OBIS names document to put in the wiki. Nicolas to check the usefulness.
- Rule frame work to be resumed.
- Establish a unique workflow for taxon name match among all functionalities with series (and possibly parallel workflow (Friday 6th). Contact Tony for discussion about the new version of TaxaMatach and IRMNG (Edward to contact Tony to get an appointment with him on Friday 6 Sept.).
- Establish the community list with whom we want to share the work (e.g., GBIF, GNA) for a further discussion, after the one with Tony. Describe the users of these tools, and how to spread it into the community in wiki. Be sure that tools can be used by external users at some point. Contact Yde to check whether we can present our taxon name matching work in a poster presentation during the TDWG meeting in October, in Firenze.
- Name reconciliation workflow: resume the work Friday 6th, not needed for the review.
Environmental variables
- Edward to re-circulate the document on priority layers of environmental parameters to be used for Species Distribution modelling (Lino, GP, Nicolas, Fabrice, Julien).
- Work in progress on Tuna and high seas.
- Bio-ORACLE deals only with surface data, and is already gridded/summarised; so it is not the type of data we were looking for. Need for looking in which cases it can be used, and look for complement in NODC (see below).
- Bio-ORACLE works in R. Further niche modeling options to be explored by Edward.
- Edward to get in touch with Fabrice (linked with first point), and explore functionality of data extraction created by TerraDue.
- Edward to organise conference call with NODC/WDC to try and learn from their experiences in creating the World Ocean Atlas out of the World Ocean Database. Implementation by CNR and/or TerraDue, to be discussed. Nicolas to check with CRIA if they are still interested in the validation part.
Identifying outliers in environmental space
- Edward explored DBScan vs LOF with help of GP. In conclusion LOF is preferred, and a report is being prepared. Issue on GP's availability to check with CNR for further work.
- Contact CRIA next week (Nicolas alone, and on Friday 6th with Edward).
Mapping proper
- Wiki to be documented with equations.
- Also test the seasonality. Edward to write a scenario on whales. Nicolas to contact Kristin Kaschner if she wants to work about this issue.
- Only write the scenario on oxygen. Wait the finalization of the seasonality page.
- Only write the scenario on tuna. Wait the finalization of the seasonality page. Although it can be included in the seasonality work.
- Work in progress about background and absence points.
- Use more and test the tools (e.g., R) within the infrastructure.
- Check that Casey is aware and test on Friday 6th.
Guidelines, Policies and Training Material
- To be done later.
- Use the R vignette style to produce such documents. Species Distribution Modelling vignette by Hijmans and Elith could serve as an example (sdm.pdf on CRAN)
Other
- Try to meet with GP on Sept. 10th.
