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# Date Author Comment
11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

11396 10/21/2013 07:14 PM Aaron Marcuse-Kubitza

fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error

11107 09/29/2013 08:58 PM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.

10866 09/04/2013 11:06 PM Aaron Marcuse-Kubitza

inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix

10619 08/07/2013 10:22 AM Aaron Marcuse-Kubitza

inputs/UNCC/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource

10618 08/07/2013 09:50 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns. reproductiveCondition: use the suggested values at DwC.vegpath.org?reproductiveCondition instead of just joining together the values in flower and fruit.

10617 08/07/2013 09:19 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: usdaRank, infrarank: documented that they should actually be mapped to infraspecificRank*. it is better to map them to taxonRank for now because infraspecificRank is now mapped to VegBIEN.

10616 08/07/2013 09:07 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: regenerated from wiki. added EQUIV (also mapped in mappings/VegCore-VegBIEN.csv).

10615 08/07/2013 09:04 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: infrarank: remapped to EQUIV (of usdaRank). usdaRank, infrarank: documented the VegCore term that each would map to.

10614 08/07/2013 08:49 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/postprocess.sql: infrarank: remove mismapped values "L." (belong in authors, and are already there)

10607 08/07/2013 05:56 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: loanto, inorout: removed mapping to occurrenceRemarks because this information does not relate to the occurrence. it is also rarely populated.

10604 08/06/2013 04:55 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/: translated single-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

10550 08/01/2013 12:43 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/new_terms.csv: regenerated

10209 07/10/2013 02:32 AM Aaron Marcuse-Kubitza

inputs/*/*/map.csv for CSV tables with a row_num column: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table

10173 07/06/2013 03:37 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: cultivated, oldGrowth: use just cultivated if it's provided, rather than /_alt-ing it back with oldGrowth (which it was generated from)

10172 07/06/2013 03:30 PM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: fixed priority of cultivated and oldGrowth so cultivated is used first if it's available

10091 06/27/2013 12:28 PM Aaron Marcuse-Kubitza

added inputs/*/*/header.csv for CSV inputs, which are now generated by inputs/input.Makefile %/install

9882 06/12/2013 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

8801 05/02/2013 08:53 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files

8264 04/01/2013 06:11 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/new_terms.csv: Updated for updated VegCore vocab

8176 03/25/2013 09:01 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: %/.map.csv.last_cleanup: Run fix_line_endings after canon/translate to standardize Python's \r\n line endings back to \n. This prevents issues with mixed line endings because LibreOffice (and probably Excel) treat all cell-internal line endings as \n but row line endings as whatever the file had, while text editors like jEdit translate all line endings to whatever the autodetected line ending is. (This creates spurious line ending diffs when a map spreadsheet containing multiline cells is edited in a text editor.)

7873 03/07/2013 06:27 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: Populated specimenHolderInstitutions

7866 03/06/2013 08:36 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.

7865 03/06/2013 08:30 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: Mapped flower, fruit -> reproductiveCondition using translation is from e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet on 2010-12-2~3

7859 03/06/2013 07:12 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: cultivated: assume anything non-NULL to be cultivated, so that we err on the side of excluding possibly-cultivated specimens

7819 03/05/2013 02:39 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true

7818 03/05/2013 02:29 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: campus: Removed mapping to occurrenceRemarks because this is just a code, not a description. Added definition from Bob's validation comments.

7817 03/05/2013 02:19 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms

7816 03/05/2013 01:56 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).

7815 03/05/2013 12:25 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder

7812 03/05/2013 11:24 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean

7811 03/05/2013 11:16 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: Fixed embedded line endings

7716 02/26/2013 05:47 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.

7713 02/26/2013 05:19 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks

7699 02/26/2013 03:44 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: herbarium->specimenIndexer: Replace UNCCD (UNCC database?) with UNCC

7663 02/26/2013 10:08 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Source: Added authors. Renamed creator to firstPublisher. Moved dataOwner to Source as list. Coordinates: latitude/longitude, coordinatePrecision: Added units disambiguation. latitude/longitude_DMS: Added components. Global IDs: Changed "globally unique" tag to "global ID" and hyperlinked it to <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs> (which now includes detailed examples of the various types of global IDs).

7646 02/22/2013 08:17 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).

7610 02/20/2013 07:33 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition

7582 02/19/2013 08:55 PM Aaron Marcuse-Kubitza

Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5

7527 02/12/2013 01:08 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.

7469 02/05/2013 04:32 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv, inputs/*/*/map.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv, which reflects the current state of the data dictionary. (Permanently switching to the new Veg+-VegCore.csv will be a separate change.) Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping and inferring units on several fields.

7433 02/04/2013 11:03 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode list->sourcename mapping: _split(): Also match ; as a separator, and match separators with or without a following space

7407 01/31/2013 06:08 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Regenerated from wiki. This adds Brad's DwC ID terms and their definitions in <https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx&gt;.

7350 01/24/2013 08:18 AM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: accession: Remapped to catalogNumber per Bob's corrections

7310 01/18/2013 12:43 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.

7198 01/11/2013 09:11 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped recordNumber to new specimenreplicate.collectionnumber

7195 01/11/2013 08:44 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped individualCode. authortaxoncode: Prefer tag over recordNumber (collectionnumber), because this applies to the plant rather than the specimen.

7190 01/11/2013 07:33 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: plantobservation: Renamed collectionnumber to authorplantcode since this number, which identifies the plant, is actually different from the collectionnumber that identifies the specimen collected from it. This distinction is meaningful for plots data, but generally not for specimens data.

7162 01/11/2013 02:03 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead

7157 01/11/2013 12:05 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: primary taxonlabel's parent taxonlabel: Fixed bug where a taxonverbatim was incorrectly being created solely to store the taxonRank, even though it was already stored in the taxonlabel's rank field

7142 01/09/2013 03:59 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.

6992 12/20/2012 02:26 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: authortaxoncode mappings: Only use authorTaxonCode if there is no plant ID, because an individual plant gets its own taxonoccurrence and thus needs the taxonoccurrence's IDs to be unique to the plant, regardless of what the author designates as the taxonoccurrence code

6989 12/20/2012 01:23 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped authorTaxonCode

6795 12/11/2012 11:41 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Removed mapping to sourcename.matched_source_id, which is now autopopulated. Split any list of institutionCodes apart using new _split().

6791 12/11/2012 11:11 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)

6756 12/11/2012 04:37 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)

6432 11/24/2012 01:24 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()

6409 11/24/2012 08:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source

6406 11/24/2012 07:50 AM Aaron Marcuse-Kubitza

db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names

6403 11/24/2012 07:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()

6384 11/24/2012 04:19 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium

6375 11/24/2012 02:10 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy

6359 11/21/2012 11:05 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name

6317 11/19/2012 07:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped oldGrowth

6314 11/19/2012 07:36 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

6313 11/19/2012 07:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

6294 11/19/2012 04:09 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

6179 11/14/2012 06:30 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata

6171 11/14/2012 05:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id

6149 11/13/2012 06:23 PM Aaron Marcuse-Kubitza

specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider

6084 11/08/2012 02:48 PM Aaron Marcuse-Kubitza

Updated inputs/UNCC/Specimen/test.xml.ref inserted row count

6035 11/06/2012 03:23 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Always map taxonNameOrEpithet to taxonomicname, now that it's globally unique at all ranks in the datasource that provides it (NCBI)

5958 11/01/2012 10:39 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched place: Also map verbatim place's geoscrub-related fields to the matched place, to link up with geoscrub's corresponding input place

5953 11/01/2012 10:09 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Renamed creator_ids to reference_id since they are now fkeys to reference

5952 11/01/2012 10:04 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Made creator_ids an fkey to reference instead of party, so that datasources are stored separately from people and to allow adding reference-type metadata (URL, copyright, etc.) for each datasource

5948 11/01/2012 09:36 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonverbatim: Renamed binomial to taxonname because this field is actually the taxonomic name without the author, not just the genus+specific epithet binomial

5947 11/01/2012 09:29 AM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Renamed *Binomial to *TaxonName because this field can store more ranks than just the genus+specificEpithet binomial (that goes in speciesBinomial)

5932 11/01/2012 07:18 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched taxonlabel's ancestors: Only create the cross links to NCBI if the name is accepted (taxonIsCanonical)

5855 10/30/2012 09:54 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed placepath to place since this contains primary information about the place, including the reference to the canonical place

5790 10/25/2012 04:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Only prepend the family to the concatenated scientificName for TNRS if it ends in -aceae (using _taxon_family_require_std()), to avoid sending unsupported, nonstandard families to TNRS which it will place in Unmatched_terms

5788 10/25/2012 04:09 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Prepend the family to the concatenated scientificName input to TNRS, so that TNRS can use it to disambiguate the genus

5783 10/25/2012 12:45 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonverbatim: Renamed species to specific_epithet to avoid confusion with the scientific meaning of species (genus+specificEpithet), since this field contains just the specific epithet

5743 10/23/2012 11:15 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Do not include rank in the mapping because taxonomicname is globally unique, and thus it isn't used in looking up the NCBI taxonlabel

5741 10/23/2012 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Also attach TNRS genus to NCBI backbone. This causes attachment to be made with as many of family and genus as are provided and have an entry in NCBI.

5739 10/23/2012 10:39 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Instead of connecting the acceptedFamily to the NCBI backbone, connect the family for the TNRS matched taxonlabel. This connects more families and also connects the same set of fields as will be connected for the genus.

5733 10/23/2012 08:42 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonName->taxonepithet: Use new _taxonomic_name_is_epithet() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field

5731 10/23/2012 08:33 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonName->taxonomicname: Use new _has_taxonomic_name() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field

5730 10/23/2012 08:30 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonName->taxonomicname: Use new _has_taxonomic_name() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field

5727 10/23/2012 08:01 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: _is_higher_taxon() calls: Default to true if the rank can't be parsed to a taxonrank enum value

5688 10/19/2012 06:15 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonName: Place it in taxonomicname instead of taxonepithet for lower taxa, because the only datasource that currently provides this field (NCBI) actually provides the full taxonomicname instead of the epithet at the current rank for lower taxa. (taxonomicname is not applicable to higher taxa because their names are not guaranteed to be globally unique.) taxonName may need to be renamed and/or redefined to account for this ambiguity in NCBI's usage.

5657 10/18/2012 04:21 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Link taxondetermination to taxonverbatim (which is a subclass of taxonlabel) instead of directly to taxonlabel. This will enable later having multiple taxonverbatims for one taxonlabel.

5656 10/18/2012 04:04 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: Renamed identifyingtaxonomicname to taxonomicname because the taxonomicname provided by the datasource is now in taxonverbatim, so there is no name collision. Note that both of these fields store the same type of information, but taxonlabel's is autogenerated while taxonverbatim's is verbatim (and is only set if provided by the datasource).

5655 10/18/2012 03:57 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: Moved non-scoping fields to new taxonverbatim subclass table, which contains the component parts of the taxonlabel

5646 10/18/2012 01:51 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Also create the identifyingtaxonomicname on the verbatim taxonlabel supplied by the datasource, in addition to on the TNRS input taxonlabel that the verbatim taxonlabel is matched up with

5645 10/18/2012 01:46 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Expanded brace expressions for putting together the identifyingtaxonomicname

5644 10/18/2012 01:21 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Always generate the concatenated identifyingtaxonomicname, even for higher taxa, to ensure that this field is always populated. Note that this will cause names of higher taxa to be scrubbed by TNRS, but this is usually not a problem because such names either have no match or not a close enough match based on the name only. Naming conventions generally cause names at different ranks to be different, so that collisions with lower ranks should not be a problem.

5638 10/18/2012 12:25 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: Renamed taxonomicname to binomial because it excludes the author

5631 10/18/2012 11:57 AM Aaron Marcuse-Kubitza

mappings: Renamed *scientificName to *binomial because DwC defines the scientificName as "The full scientific name, with authorship and date information if known", but many datasources do not include the author in their scientific name, and the fields scientificName is mapped to in VegBIEN assume it does not include the author

5608 10/17/2012 04:12 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed taxonconcept to taxonlabel per today's conference call, where it was decided that taxonconcept contained too many unrelated fields to be purely a taxon concept

5596 10/17/2012 12:43 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Renamed taxonname to taxonepithet for clarity and to be consistent with TCS's use of "epithet" to denote what the taxonname was intended to be (http://www.tdwg.org/standards/117/download/#/UserGuidev_1.3.pdf)