mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.
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).
mappings/VegCore.htm: regenerated from wiki. merged confusingly-named TaxonObservation into TaxonOccurrence. added project_participant.
mappings/VegCore.htm: regenerated from wiki. added taxon_determination__is_current, taxon_determination__is_original.
mappings/VegCore.htm: regenerated from wiki. added Stratum table.
mappings/VegCore.htm: regenerated from wiki. added source__version (= edition), source__modified_date.
mappings/VegCore.htm: regenerated from wiki. added dayOfYear (=julianDay), which is different from startDayOfYear/endDayOfYear.
mappings/VegCore.htm: Regenerated from wiki
mappings/VegCore.htm: Regenerated from wiki. Added flower, fruit, commonName.
mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.
mappings/VegCore.htm: Regenerated from wiki. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.
mappings/VegCore.htm: Regenerated from wiki. Taxon: Moved scrubbing-related terms to MatchedTaxon.
mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).
mappings/VegCore.htm: Regenerated from wiki. Editing: Changed ambiguous terms templates to list the name of the alternative itself in the alternatives list, instead of the ambiguous term + a source suffix. This avoids the need to choose a source suffix for each alternative of an ambiguous term, as the ambiguous term itself (without the suffix) can be listed as the synonym. Coordinates: Disambiguated verbatimCoordinateSystem.
mappings/VegCore.htm: Regenerated from wiki. Split apart identificationQualifier and taxonFit. Split apart taxonConfidence and identificationVerificationStatus. Moved identificationQualifier to new QualifiedTaxonName table.
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.
mappings/VegCore.htm: Regenerated from wiki. latitude/longitude: Moved _deg,min,sec components after unit alternatives so that unit alternatives following them wouldn't incorrectly be interpreted as alternatives for the *components instead of for the overall, unitless term.
mappings/VegCore.htm: Regenerated from wiki. Merged coordinateUncertainty and coordinatePrecision, since datasources often use these interchangeably (the only difference is the DwC-recommended units).
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).
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).
mappings/VegCore.htm: Regenerated from wiki. verbatimScientificName, verbatimTaxonName have been merged into concatenatedScientificName, and ID has been disambiguated.
mappings/VegCore.htm: Regenerated from wiki. matched*Fit_fraction has been renamed to matched*Confidence_fraction.
mappings/VegCore.htm: Regenerated from wiki. Data owner terms and taxon synonyms have been added, and morphospecies has been disambiguated.
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.
mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term
mappings/VegCore.csv: Regenerated from wiki. Alternatives are now able to use h3 instead of h4 (which had display problems). realLatitude/Longitude is now no longer needs the ? prefix to have its replacement (PRIVATE) interpreted as an alternative, and thus is properly able to be included in the vocabulary.
Renamed mappings/VegCore.csv to VegCore.vocab.csv and Veg+-VegCore.csv to VegCore.thesaurus.csv for clarity
mappings/Makefile: Veg+-VegCore.csv: Sort terms by name so that reordering terms in the VegCore data dictionary does not cause Veg+-VegCore.csv to change. This makes it much easier to identify synonyms and ambiguous terms that were accidentally deleted during a data dictionary refactoring. (Note that these are no longer included in VegCore.csv, so this is required in addition to sorting VegCore.csv by name.)
mappings/VegCore.csv: Regenerated from wiki. This adds cf_aff.
mappings/VegCore.csv: Regenerated from wiki. This causes TNRS's Annotations (cf/aff) to be mapped into VegBIEN.
mappings/Makefile: Veg+-VegCore.csv: Generate dynamically from VegCore.htm, which allows the VegCore thesaurus to be automatically kept up to date. More importantly, it allows terms in all map spreadsheets to be updated simultaneously when a term is renamed (e.g. by replacing a term with one of its synonyms).
mappings/Veg+-VegCore.csv: Removed Sources, Definition columns because source information is now in the VegCore data dictionary
mappings/Veg+-VegCore.csv: Separate alternatives of ambiguous terms with , instead of ", " for easier machine-parsability
mappings/Veg+-VegCore.csv: Sources: Removed redundant bien2_ prefix from bien2_staging subnamespace
mappings/Veg+-VegCore.csv.csv: Removed hypothetical terms which are not in use by any VegBIEN datasource
mappings/Veg+-VegCore.csv: habit: Remapped to growthForm, which replaces verbatimGrowthForm
mappings/VegCore.csv: BIEN2 terms: Added sub-namespaces (bien_web, geoscrub, etc.) to source URLs
mappings/VegCore.csv: Terms: Removed namespace prefixes (dcterms:), because VegCore terms are globally unique within VegCore and there should not be multiple versions of the same VegCore term with different namespaces. Provenance is instead indicated in the Sources column, which contains not just a namespace but a full URL to each source term.
mappings/VegCore.csv: Term names: Changed special characters to _ because Redmine doesn't support special characters in HTML anchors (it removes everything except letters, numbers, _, and -)
mappings/VegCore.csv, Veg+-VegCore.csv: obs*Date: Re-sourced to VegX:obs*Date
mappings/VegCore.csv, Veg+-VegCore.csv: Removed the additional dict namespace for the SALVIAS sources. This removes the extra "dict:" namespace on the generate Redmine source term names.
mappings/VegCore.csv, Veg+-VegCore.csv: Added TNRS provider namespace, inserting it before BIEN in the sort order
mappings/VegCore.csv, Veg+-VegCore.csv: Removed the additional BIEN namespace for the BIEN sources, and use just BIEN2 and VegBIEN as the sub-namespaces. This removes the extra "BIEN:" namespace on the generate Redmine source term names.
mappings/VegCore.csv, Veg+-VegCore.csv: Removed the "terms" text in the current DwC terms' provider, and leave just the sort order. This removes the extra "terms:" namespace on the generate Redmine source term names.
mappingsf/VegCore.csv, Veg+-VegCore.csv: Renamed Comments to Definition to match Redmine table
mappings/VegCore.csv, Veg+-VegCore.csv: Reversed order of Comments, Sources columns to match Redmine table order
mappings/VegCore.csv, Veg+-VegCore.csv: Renamed Source column to Sources because it can contain multiple sources
mappings/VegCore.csv, Veg+-VegCore.csv: Source: DwC terms: Scoped sort order by category, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_refactoring#Scope-DwC-sort-order-by-category>
mappings/VegCore.csv, Veg+-VegCore.csv: Source: VegX terms: Split combined field group/field sort order into separate sort orders for field and field group
mappings/VegCore.csv, Veg+-VegCore.csv: Source: VegX terms: Added top-level table sort order
mappings/VegCore.csv, Veg+-VegCore.csv: Source: DwC occurrenceID: Corrected sort order to 019 instead of 000
mappings/VegCore.csv, Veg+-VegCore.csv: Source: DwC terms: Added category, with category sort order, as URL comment. This will allow terms to be sorted just within their category rather than globally for DwC.
mappings/Veg+-VegCore.csv: Source: DwC: dcterms: Added back "dcterms:" prefix to URL fragment
mappings/VegCore.csv, Veg+-VegCore.csv: Removed no longer used Order within table column. Instead, embed the sort order in the URL using a () comment.
mappings/VegCore.csv, Veg+-VegCore.csv: Merged the Order within table column with the Source URL, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_refactoring#Merging-the-Order-within-table-column-with-the-Source-URL>. Sorting on the Source column now groups related terms together according to their sort order in the source they came from.
mappings/Veg+-VegCore.csv: Order within table: Filled in missing sort orders
mappings/VegCore.csv, Veg+-VegCore.csv: Source: Web pages: Use / instead of . to separate nested elements of URL fragment. Use _ instead of + to represent space.
mappings/VegCore.csv, Veg+-VegCore.csv: Sources: BIEN2: Moved DB sort order right before the DB name in the URL to avoid duplicating the DB name in the comment
mappings/VegCore.csv, Veg+-VegCore.csv: Sources: Added sort order comments to URLs so they sort in the order indicated at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Sources>. URL comments are enclosed in (), and the sort order element of a comment is a number right after the ( .
mappings/Makefile: .Veg+-VegCore.csv.last_cleanup: Sort by the source URL instead of the VegCore term
mappings/Veg+-VegCore.csv: Removed type->dcterms:type automapping because this term can have many different meanings
mappings/VegCore.csv: Renamed plotName to locationName because this term also applies to the location of a specimen. This replaces CTFS's definition of locationName as locality.
mappings/Veg+-VegCore.csv: Added height
mappings/Veg+-VegCore.csv: cationExchangeCapacity->cationExchangeCapacity_cmol_kg mapping: Removed ? prefix because a mapping to only one set of units is unambiguous (if additional units for cationExchangeCapacity are found, this will become an ambiguous mapping). Note that canon automatically removes punctuation from VegCore terms, so this mapping would previously have had the ? prefix autoremoved anyway (both in inputs/*/*/map.csv and recently also in Veg+-VegCore.csv).
mappings/Veg+-VegCore.csv: Prefix ambiguous terms' VegCore replacement with "?" so it's visually flagged in map.csv, in the same way that unmatched terms are flagged with a "*" prefix
mappings/Veg+-VegCore.csv: Soil component measurements: Added unitless terms that automap to all alternatives of units
mappings/Veg+-VegCore.csv: Remapped latitude/longitude to decimalLatitude/Longitude because these fields almost always have units of decimal degrees
mappings/Veg+-VegCore.csv: DBH: Removed diameterBreastHeight_m alternative because datasources that don't append units to DBH almost always have units of cm or in
mappings/VegCore.csv: Added diameterBreastHeight_in
mappings/Veg+-VegCore.csv: Remapped DBH from no longer existing term diameterBreastHeight to diameterBreastHeight_cm, diameterBreastHeight_m (both terms will be listed in the map spreadsheet after automapping, and the user can then choose one)
mappings/Veg+-VegCore.csv: Added parentPlotID
mappings/Veg+-VegCore.csv: Removed redundant stem_id->stemID mapping
mappings/Veg+-VegCore.csv: Standardized the capitalization of names, by camel-casing each name except for acronyms and "ID", which are made all uppercase
mappings/Veg+-VegCore.csv: Added sources where missing
mappings/Veg+-VegCore.csv: Added Source and Comments columns from mappings/Veg+.terms.csv. Reordered columns to put Comments first.
mappings/Veg+-VegCore.csv: Remapped realLatitude, realLongitude to new special value PRIVATE, which is more specific than OMIT
mappings/Veg+-VegCore.csv: Mapped realLatitude, realLongitude to OMIT because private data should not be placed in a public database
mappings/Veg+-VegCore.csv: Removed inaccurate SizeOfSite->plotArea mapping, which does not match units
mappings/Veg+-VegCore.csv: Remapped subspecies, subSpeciesName to new subspecies term
mappings/Veg+-VegCore.csv: Changed output column header from Veg+ to VegCore because this is more accurate. This is possible now that we're using new automapping scripts that do not require a particular column header. Note that this change now requires the map.csvs to use VegCore as their output column header, because otherwise the Veg+ header will get automapped to VegCore. (The header replacing is a feature to support changing the header when the schema of the column's terms changes.)
mappings/Veg+-VegCore.csv: Removed no longer used Comments column. Use mappings/Veg+.terms.csv to cite term definitions instead.
mappings/Veg+-VegCore.csv: previousCatalogNumber: Removed no longer needed "According to" comment, because this is now documented in the mappings/Veg+.terms.csv entry. Note that the citation for any mapping is the overlap of the terms' definitions, and thus only the definitions need to be cited, not the mapping itself. (The definitions are provided in the links in mappings/Veg+.terms.csv.)
mappings/Veg+-VegCore.csv: Remapped QuadratID to subplotID because the standard definition of an ID term is an ID that's unique within the datasource, and it's just CTFS's usage that makes it unique only within the plot
mappings/Veg+-VegCore.csv: Removed recordNumber/_alt and recordNumber redirection mappings so that Veg+-VegCore.csv contains only renamings, not business logic. Note that removing the global ordering of these fields does not affect the datasources which contain multiple recordNumber synonyms because they either have a custom ordering or one field is duplicated or unused.
mappings/Veg+-VegCore.csv: DescriptionOfSite: Mapped directly to locality rather than to locationNarrative to avoid needing multiple levels of mappings to get to the VegCore term
mappings/Veg+-VegCore.csv: Removed scientificNameAuthorship/_alt and scientificNameAuthorship redirection mappings, which were only used by SpeciesLink but it now has the necessary _alts in its own map.csv
mappings/Veg+-VegCore.csv: Removed dateCollected/_alt and dateCollected redirection mappings, which were only needed when multiple dateCollected fields were being combined in Veg+-VegCore.csv
mappings/: Moved year/month/dayCollected mappings from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic. Note that this allows the year/month/dayCollected values to bypass the additional _dateRangeStart filter that is applied to text dates. The priority of the plain dateCollected field is now higher than the year/month/dayCollected fields when both are specified, because the dateCollected field presumably contains verbatim text while the year/month/dayCollected fields contain parsed date parts.
mappings/Veg+-VegCore.csv: Removed dateIdentified/_alt and dateIdentified redirection mappings, which were only needed when multiple dateIdentified fields were being combined in Veg+-VegCore.csv
mappings/: Moved year/month/dayIdentified mappings from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic. Note that this allows the year/month/dayIdentified values to bypass the additional _dateRangeStart filter that is applied to text dates. The priority of the plain dateIdentified field is now higher than the year/month/dayIdentified fields when both are specified, because the dateIdentified field presumably contains verbatim text while the year/month/dayIdentified fields contain parsed date parts.
mappings/: Moved verbatimGrowthForm filter mapping from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic
mappings/Veg+-VegCore.csv: Remapped CTFS QuadratID to subplot rather than subplotID, because it's only unique within the parent plot, not globally unique, in CTFS
mappings/Veg+-VegCore.csv: Mapped speciesInvID
mappings/Veg+-VegCore.csv: Mapped stem_id
mappings/Veg+-VegCore.csv: Mapped speciesName, subSpeciesName
mappings/Veg+-VegCore.csv: Mapped stemTag
mappings/Veg+-VegCore.csv: Mapped DBH
mappings/VegCore-VegBIEN.csv: Removed no longer used parentLocationID, parentPlotName (locationID and plotName now automatically map to the correct location). mappings/Veg+-VegCore.csv: Removed no longer used parentPlotID.
