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 DUPLICATE.
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. Added specimenDescription.
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/Makefile: VegCore.vocab.csv: Ignore leading ? when sorting so that ambiguous terms sort alphabetically with other terms. This prevents terms from moving from their previous location when they become ambiguous.
mappings/VegCore.vocab.csv: Changed line endings to \r\n in preparation for having a Python script run on it (which changes the line endings)
mappings/Makefile: VegCore.vocab.csv: Added back ambiguous terms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are ambiguous or unambiguous terms
mappings/Makefile: VegCore.vocab.csv: Added back synonyms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are synonyms or primary terms. This also prevents VegCore.vocab.csv from losing entries when terms are renamed, which made it difficult to verify that no terms were lost when refactoring.
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).
Renamed mappings/VegCore.csv to VegCore.vocab.csv and Veg+-VegCore.csv to VegCore.thesaurus.csv for clarity
mappings/Makefile: VegCore.csv: Sort terms by name so that reordering terms in the VegCore data dictionary does not cause VegCore.csv to change. This makes it much easier to identify terms that were accidentally deleted during a data dictionary refactoring.
mappings/Makefile: VegCore.csv: Fixed bug where need to remove duplicates, which are no longer supported by canon, by removing alternatives of ambiguous terms when these occur separately from their definitions
mappings/Makefile: VegCore.csv: Removed synonyms and ambiguous terms, since the canonicalization of them is handled by Veg+-VegCore.csv. This also reduces the time it takes canon to build the in-memory Python dict of replacements, which scales to all inputs and should speed up the build/test command.
mappings/Makefile: VegCore.csv: Removed synonyms, since the canonicalization of them is handled by Veg+-VegCore.csv
mappings/Makefile: VegCore.csv: Match terms by header # instead of matching all anchors, in order to include the leading ? before an ambiguous term
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.
mappings/Makefile: VegCore.csv: Include only terms that start with a lowercase letter or are all caps. This also avoids the need to filter out VegCore.tables.csv.
mappings/VegCore.csv: Changed line endings to \n in preparation for not running filter_out_cs on the file (which changes line endings to \r\n)
mappings/Makefile: VegCore.csv: Filter out the VegCore tables so they are not matched as terms. This is necessary because some terms have the same name as a table, but the term should be the match rather than the table.
mappings/VegCore.csv: Changed line endings to \r\n to match the output of filter_out_ci
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)
mappings/VegCore.csv: Changed line endings to \n to match what sed generates from the VegCore data dictionary page
mappings/VegCore.csv: Removed informational columns, because this information is now maintained on the VegCore data dictionary page at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore>
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: Removed no longer used verbatimGrowthForm. Use growthForm instead.
mappings/VegCore.csv: UNUSED: Comments: Added Redmine formatting
mappings/VegCore.csv: OMIT: Changed "is omitted" to "should be omitted", because the mappings specify suggestions rather than requirements as to how a field should be used
mappings/VegCore.csv: Removed no longer used subInstitutionCode. Use datasource, institutionCode instead.
mappings/VegCore.csv: Added datasource
mappings/VegCore.csv: referenceType: Added closed list values
mappings/VegCore.csv: observationMeasure: Re-sourced to SALVIAS:observation_type, since SALVIAS comes before VegBIEN in the source precedence
mappings/VegCore.csv: Renamed sampleType to observationType to match the SALVIAS term it's derived from
mappings/VegCore.csv: Added individualCount_*cm_or_more used by analytical_aggregate
mappings/VegCore.csv: subplotX/Y: Added definition
mappings/VegCore.csv: subplot*: Sources: Put SALVIAS:subplot last, because the specific field is closer in meaning to the term than the category
mappings/VegCore.csv: project*Date: Added definition
mappings/VegCore.csv: parentPlotName: Added definition
mappings/VegCore.csv: parent*: Sources: Put VegBank:PARENT_ID last, because the specific field is closer in meaning to the term than the category
mappings/VegCore.csv: locationName: Added definition
mappings/VegCore.csv: eventDate/startDate/endDate: Added definition
mappings/VegCore.csv: locationName: Sources: Put VegX:plotName first because it is closest in meaning to the term
mappings/VegCore.csv: recordedBy*: Added definition
mappings/VegCore.csv: recordedBy.middleName: Added source to DwC:recordedBy
mappings/VegCore.csv: soil composition terms: Removed ppm units from the definition, since units are actually fraction or percent
mappings/VegCore.csv: Comments: Added quotes around quotations from other sources
mappings/VegCore.csv: Definitions: Added quotes around quotations from other sources
mappings/VegCore.csv: VegX terms without definitions in VegX: Added definitions from non-VegX sources, etc.
mappings/VegCore.csv: height_ft: Added source to VegBank:stemHeight, which includes a description of the term
mappings/VegCore.csv: height_m: Added source to VegBank:stemHeight, which includes a description of the term
mappings/VegCore.csv: projectName: Added definition from VegX schema
