0.1.4

Features

n/a

Improvements

• added support for NCBI purl prefixes (e.g., http://purl.obolibrary.org/obo/NCBITaxon_9606)
• added support for long GBIF taxon prefixes (e.g., https://www.gbif.org/species/110462373)
• upgrade apache common-compress lib to v1.18
• upgrade default GloBI taxon graph to point to https://zenodo.org/record/1466011
• improve documentation

Bug fixes

n/a

0.1.3

Features

n/a

Improvements

• added jar magic for easy install and running on mac/linux
• add cross-ref-doi matcher
• add pubmed id to doi resolver
• upgrade globi libs
• add output schema support for id, name and rank

Bug fixes

• prevent npe on empty paths in rank based export schema

0.1.2

Features

n/a

Improvements

• exposed stop word and name translators via remove-stop-words and translate-names matchers.
• move globalnames api wrapper into nomer from https://github.com/jhpoelen/eol-globi-data
• make stop word and name translators configurable, point to https://github.com/globalbioticinteractions/globi-taxon-names for defaults

Bug fixes

• create cache dir if it not yet exists
• allow for printing input-schema

0.1.1

Features

n/a

Improvements

• added taxonomic name mappings provided by @BrianHayden and collaborators.

Bug fixes

n/a

0.1.0

Features

• Introduce command replace to replace matched values according defined schemas. By default, input expects ids in first columns and names in second. The output schema is the same. Added examples in readme.
• Introduce matcher globi-taxon-rank. This matcher takes taxonomic rank names and attempts to match them against wikidata taxon rank items. Wikidata itself is mined for "common names" for taxonomic ranks in various languages. The taxonomic rank information is cached locally after first use.
• Exposed individual matchers used by globi-enrich matcher. These include but are not limited to taxonomic lookup at Atlas of Living Australia, National Biodiversity Network, NCBI, ITIS, EOL, WoRMS and more.
• Added a stopword remover as part of the globi-correct matcher.

Improvements

• Various updates to documentation.
• Added more information to the output of the matchers command.
• Point default taxon cache to GloBI Taxon Cache 0.3.2 at http://doi.org/10.5281/zenodo.1250572 .
• Remove progress reporting with .. Probably best to use a program like pv in combination with *nix pipes to report on progress.
• Upgrade to globi libs v0.9.18 .

Bug fixes

• make sure to include empty ncbi taxon path/id/rank elements to avoid inconsistent taxonomic path lengths.

0.0.7

Features

1. introduce commands validate-term and validate-term-link to add support for term (aka TaxonCache) and term link (aka TaxonMap) validation (see #8 and #5)
2. introduce command append-json to add preliminary support for term match output in json (see #7 )

Improvements

1. support NCBITaxon: and BioGoMx: prefixes

Bug fixes

n/a

0.0.6

Features

1. make max term links configurable

Improvements

1. improve term matching performance by settings reasonable defaults

Bug fixes

1. version did not print correctly due to jar shadowing, now using package implementation version instead.

0.0.5

Features

Improvements

1. let system properties override default properties
2. add documentation regarding reproducing outcomes

Bug fixes

1. close property file handles to avoid to many open files error
2. fix test error by updating assertions related to iNaturalist taxon hierarchy.

0.0.4

Features

1. add ability to configure through property files
2. add ability to define an input schema, pointing at name/id columns.
3. add command to clean cache
4. add command to list properties

Improvements

Bug fixes

0.0.3

Features

1. bootstrap NODC taxonomy if not available in cache
2. introduce ability to select specific term matchers (e.g., globi-globalnames, globi-enrich, globi-correct)

Improvements

1. move taxon / name specific modules from https://github.com/jhpoelen/eol-globi-data into nomer

Bug fixes