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 EventParticipant table containing event__participant.
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 EQUIV (also mapped in mappings/VegCore-VegBIEN.csv).
mappings/VegCore.htm: regenerated from wiki. added dayOfYear (=julianDay), which is different from startDayOfYear/endDayOfYear.
mappings/VegCore.htm: regenerated from wiki. Special terms: added instructions for adding a distinguishing suffix to each special term in the format special_term#suffix. this is needed for new-style import to make the resulting column name unique within the staging table.
mappings/VegCore.htm: regenerated from wiki. Special terms: added DUPLICATE.
mappings/VegCore.htm: regenerated from wiki. moved UNUSED, PRIVATE underneath OMIT as subterms.
mappings/VegCore.htm: Regenerated from wiki
mappings/VegCore.htm: Renamed salvias_plots table plotMetadata to PlotMetadata because of SALVIAS refresh on nimoy
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. Renamed MatchedTaxonDetermination/AcceptedTaxonDetermination to MatchedTaxon/AcceptedTaxon because they relate to a taxon name rather than to an application of that name to a TaxonOccurrence
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. Added specimenDescription.
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. Moved Forming IDs section to separate Global IDs wiki page (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs).
mappings/VegCore.htm: Regenerated from wiki. Moved preferred ID order to Forming IDs section as examples list. Made examples globally unique by prefixing the outer ID that scopes the value.
mappings/VegCore.htm: Regenerated from wiki. Forming IDs: Added instructions for making a local ID global. Added note that these globally unique IDs are not the same as UUIDs. Forming preferred IDs: Reworded as a set of instructions rather than a definition. Clarified that this becomes the database primary key.
mappings/VegCore.htm: Regenerated from wiki. Added section on forming preferred IDs, which are the ID which is most directly associated with the identified object.
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.htm: Regenerated from wiki. The original*, accepted*, and verbatim* Taxon fields have now been moved to separate OriginalTaxonDetermination, AcceptedTaxonDetermination, and TaxonVerbatim tables.
mappings/VegCore.*.csv: Regenerated from wiki. A plain text label is now used for Replace with, which fixes a bug where the PRIVATE permalink pointed to its Replace with in realLatitude instead of its definition.
mappings/VegCore.*.csv: Regenerated from wiki. Alternatives now contain the "Alternative" label as plain text rather than as an image title, thus avoiding an HTML anchor conflict with the definition and allowing ambiguous terms to be placed before their alternatives as well as after.
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.
mappings/VegCore.csv: Regenerated from wiki. The data dictionary has been reformatted to be much more vertically compact, by placing the term type (Synonym, Alternative, etc.) and sources (From:) on the same line as the term. Note that globalUniqueIdentifier_SpeciesLink has been removed from the vocabulary because a definition entry has been added for it (when this entry is missing, the term is incorrectly identified as a primary term).
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/VegCore.csv: Regenerated from wiki. All synonyms are now hyperlinked, allowing them to be matched by redmine_synonyms.
mappings/VegCore.csv: Regenerated from wiki. Ambiguous terms newly available to redmine_synonyms due to the bugfix now have multiple alternatives.
mappings/VegCore.csv: Regenerated from wiki. All ambiguous terms now have multiple alternatives, preventing them from being automapped to a single alternative without prompting the user for confirmation
mappings/VegCore.csv: Regenerated from wiki. All mappings/Veg+-VegCore.csv terms are now added as synonyms or separate terms.
mappings/VegCore.csv: Regenerated from wiki. Most ambiguous terms are now split into alternatives, and most mappings/Veg+-VegCore.csv terms are now added as synonyms.
mappings/VegCore.csv: Regenerated from wiki
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>.
mappings/VegCore.csv: Regenerated from wiki. Synonym lists have now been translated to sections to create a web page anchor for each synonym, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore_refactoring#Index-synonyms-as-web-page-anchors>. This enables searching for VegCore synonyms in the data dictionary as well as terms, and makes it possible to swap a term and a synonym while still keeping both as indexed anchors.
mappings/VegCore.csv: Regenerated from wiki. All uncategorized terms have now been moved to tables.
Regenerated mappings/VegCore.htm
Regenerated mappings/VegCore.csv, which adds categories
mappings/Makefile: Generate VegCore.csv from the VegCore data dictionary page by extracting all HTML anchors (in Redmine, each section heading, and therefore each VegCore term, gets its own anchor)
