Activity
From 11/28/2011 to 12/27/2011
12/22/2011
- 12:41 PM Task #302: Make changes to VegBIEN schema
- Bob Peet's changes are at [[VegBIEN from VegBank]]
E-mail from Bob Peet on 2011-12-22:
I promised to summarize ... - 12:31 PM Task #310 (Resolved): automated build process
- I set up an automated build process for all the BIEN scripts and dependencies. It runs on both vegbiendev and nimoy. ...
- 12:31 PM Task #310 (Resolved): automated build process
12/16/2011
- 12:31 PM Task #300: TurboVeg data
- Mike Lee's mapping is on nimoy under @/home/bien_shared/raw_data/turboveg/DBASEDIC_rkp2011_mtl2011.xlsx@
- 12:21 PM Task #309 (Rejected): mapping and export utility from VegBank to VegX
- Ideally, what I have in mind is mapping and export utility from VegBank to VegX. Of course this means more work up fr...
- 12:20 PM Task #308 (Resolved): do a direct transfer of some public data from VegBank
- Even higher priority, do you think you could set us up to do a direct transfer of some public data from VegBank? At t...
12/15/2011
- 03:42 PM Task #307 (Resolved): Acquire additional specimen data sets in both DwC and DwCA format, esp. GBIF
- 03:42 PM Task #306 (Resolved): Acquire additional plot data sets from providers willing to work with Aaron on mappings and validations
- Bob: TurboVeg; Brad: RAINFOR, CTFS
- 03:42 PM Task #305 (Resolved): Complete full-dataset validations for NYBG & SALVIAS
- 03:41 PM Task #304 (Resolved): Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
- * Identify and make changes to VegX needed to enable full-dataset imports
* Or report changes needed to Nick, Miquel... - 03:41 PM Task #303 (New): Mapping from VegBIEN to original VegBank
- the latter to be used as web schema for BIEN web interface
- 03:40 PM Task #302 (Resolved): Make changes to VegBIEN schema
- 02:49 PM Task #294: find plot data source provider to work with Aaron
- Brad has contacted two data source provider (RAINFOR, CTFS) regarding working with Aaron to develop mappings
- 01:55 PM Task #285 (Resolved): CSV to XML mappings for NYBG, SALVIAS
- initial data sources NYBG and SALVIAS have been fully mapped
- 01:53 PM Task #291 (Resolved): list of milestones
- got commented milestones from Martha
- 01:03 PM Task #286: CSV-XML-database mapping script
- I added support for mapping XML to XML, which will enable us to process NVS's VegX data, and eventually also their in...
- 01:03 PM Task #296: Direct mapping from native salvias_plots MySQL database to VegBIEN
- I added a new mapping to get SALVIAS data directly from the salvias_plots database on nimoy. You can see the results ...
12/14/2011
- 02:29 PM Task #299: Mapping from NVS to VegX and VegBIEN
- NVS data from Nick Spencer is on nimoy in @/home/bien_shared/raw_data/nvs/@
- 02:06 PM Task #299 (Resolved): Mapping from NVS to VegX and VegBIEN
- Will require finding someone at NVS willing to work with Aaron and mappings and validations
- 02:25 PM Task #300: TurboVeg data
- TurboVeg info from Bob Peet is on nimoy in @/home/bien_shared/raw_data/turboveg/@
- 02:07 PM Task #300 (New): TurboVeg data
- with commitment by someone familiar with DB to work with Aaron on (a) evaluating mappings, and (b) developing validat...
- 02:07 PM Task #301 (Resolved): RAINFOR data
- with commitment by someone familiar with DB to work with Aaron on (a) evaluating mappings, and (b) developing validat...
- 02:06 PM Task #298 (New): Try to find source of DwCA (DwC Archives) data
- hoping GBIF will be willing to work with us on this. Possibly approach Remsen directly
- 02:05 PM Task #297 (Resolved): Request new data dump of specimen data from GBIF, this time in DwC format
- 02:03 PM Task #296 (Resolved): Direct mapping from native salvias_plots MySQL database to VegBIEN
- 01:59 PM Task #289: look for formal mapping mechanism
- Got NVS mapping tool from Nick Spencer, which is on nimoy in @/home/bien_shared/raw_data/nvs/VegX/@
- 01:54 PM Task #286: CSV-XML-database mapping script
- Added support for database and XML inputs
12/13/2011
- 12:11 PM Task #295 (Resolved): provide benchmark queries for NYBG data
- Brad Boyle provided NYBG queries, which are on the wiki under [[NYBG tests]]
- 12:10 PM Task #290: benchmark tests for database loading
- Brad Boyle provided NYBG queries, which are on the wiki under [[NYBG tests]]
- 11:57 AM Task #291: list of milestones
- updated to do list
- 11:56 AM Task #291: list of milestones
- Brad created a timeline, which is on the wiki under [[December 8 2011 WebEx meeting]].
12/08/2011
- 05:38 PM Task #285: CSV to XML mappings for NYBG, SALVIAS
- To make it easier to review the mappings, I created human-readable versions "in Subversion":https://projects.nceas.uc...
- 03:12 PM Task #295 (Resolved): provide benchmark queries for NYBG data
- 03:11 PM Task #294 (Resolved): find plot data source provider to work with Aaron
- 01:07 PM Task #290: benchmark tests for database loading
- Brad Boyle provided SALVIAS queries, which are on the wiki under [[SALVIAS tests]]
12/07/2011
- 04:05 PM Task #288: VegX-VegBank mapping
- If you would like to browse the @vegbank@ database on nimoy, you can now use "phpPgAdmin":http://bien.nceas.ucsb.edu/...
- 03:47 PM Task #293: mapping inversion script
- updated transformations
- 01:43 PM Task #293: mapping inversion script
- suggested name and location: @svn/scripts/util/invert_map@
- 01:41 PM Task #293 (New): mapping inversion script
- A Python script to invert a mapping spreadsheet. This will be useful for mapping VegBank to VegX, so that we can just...
- 02:18 PM Task #289: look for formal mapping mechanism
- *"RDF SPARQL":http://en.wikipedia.org/wiki/SPARQL:*
* SELECT-style queries for RDF data
* uses concise Turtle syn... - 02:01 PM Task #289: look for formal mapping mechanism
- *"IBM Clio":http://www.almaden.ibm.com/cs/projects/criollo/:*
* "Clio then also interprets these mappings to const... - 01:23 PM Task #289: look for formal mapping mechanism
- updated to do list
- 01:11 PM Task #289: look for formal mapping mechanism
- *"Bourret's XML-ER mapping":http://rpbourret.com/:*
* *summary: his various mapping methods are already used by Ve... - 12:45 PM Task #289: look for formal mapping mechanism
- *XQuery:*
* "XQuery Tutorial":http://www.w3schools.com/xquery/default.asp
** XQuery iterates over XML documents stor... - 12:38 PM Task #289: look for formal mapping mechanism
- *Altova XMLSpy's graphical generation of XPaths:*
* *summary: XMLSpy and Oxygen XML both have Copy XPath commands (O...
12/06/2011
- 04:34 PM Task #288: VegX-VegBank mapping
- A mostly working VegX-VegBank mapping is now available is now available in svn at https://projects.nceas.ucsb.edu/nce...
- 04:31 PM Task #287 (Resolved): XML to database conversion script (merged into CSV-XML-database mapping script)
- 04:28 PM Task #285: CSV to XML mappings for NYBG, SALVIAS
- Working NYBG-VegBank mappings are now available in svn at https://projects.nceas.ucsb.edu/nceas/projects/bien/reposit...
- 04:26 PM Task #286: CSV-XML-database mapping script
- We are now able to import NYBG data directly into VegBank, using the map2vegbank script on nimoy at @/home/bien_share...
12/05/2011
- 12:14 PM Task #292: VegBank metadata query mechanism
- (Moved to issue description)
- 12:13 PM Task #292 (New): VegBank metadata query mechanism
- For data discovery of VegBank schema.
Mike Lee's suggestion: (e-mail on 2011-11-9)
I'm wondering if you all tal... - 12:09 PM Task #289: look for formal mapping mechanism
- Mike Lee's explanation of the VegBank XML serialization format: (e-mail on 2011-12-2)
My recollection is that our in...
12/01/2011
- 04:44 PM Task #291: list of milestones
- I put the tasks from today's conference call into the "Redmine issue tracker":https://projects.nceas.ucsb.edu/nceas/p...
- 04:35 PM Task #291 (Resolved): list of milestones
- *Conference call:*
* -need list of milestones for the next 6-12 months-
* -*add conference call tasks to Redmine ... - 04:34 PM Task #290 (Resolved): benchmark tests for database loading
- *Conference call:*
* *develop benchmark tests to check that datasource data was inserted correctly into VegBank*
... - 04:32 PM Task #289 (Resolved): look for formal mapping mechanism
- *Conference call:*
* look into VegBranch's way of capturing mappings and metadata
* -look into Altova XMLSpy's gr... - 04:29 PM Task #285: CSV to XML mappings for NYBG, SALVIAS
- *Conference call:*
* Ignore SALVIAS @voucher_string@ because it is sometimes missing collector's name
* Ignore SALVI... - 10:50 AM Task #285: CSV to XML mappings for NYBG, SALVIAS
- The latest mapping spreadsheets for datasources->VegX and VegX->VegBank are now available in svn at https://projects....
- 10:53 AM Task #286: CSV-XML-database mapping script
- I've merged data2xml and xml2db into one script called map, which can be run on nimoy at /home/bien_shared/svn/script...
- 10:52 AM Task #288: VegX-VegBank mapping
- The mapping spreadsheet for VegX->VegBank is now available in svn at https://projects.nceas.ucsb.edu/nceas/projects/b...
11/30/2011
- 01:40 PM Task #288 (Resolved): VegX-VegBank mapping
- CSV spreadsheet mapping VegX to VegBank
- 01:37 PM Task #287: XML to database conversion script (merged into CSV-XML-database mapping script)
- Merged into CSV-XML-database mapping script
- 01:35 PM Task #286: CSV-XML-database mapping script
- Merged in XML to database conversion script
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