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Recent Releases of Global Biotic Interactions

Global Biotic Interactions -

Features

Improvements

Bug fixes

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Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 5 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 5 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • support interactions.csv as well as interactions.tsv to reduce friction for template datasets.

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • use disk-based treemap to reduce memory pressure when importing Darwin Core Archives
  • enable /exists endpoint for quick http status code based record existence check (see #401)
  • make "ecologically relates to", http://purl.obolibrary.org/obo/RO_0002321, default interaction type group

Bug fixes

  • make sure to re-create listener on setting import logger to ensure continued monitoring of import logs

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • use try-with-resources java construct to increase inputstream hygiene
  • disable jar cache to avoid leaking file descriptors for dataset archives
  • upgrade to commons-io 2.6

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • replace deprecated neo4j transaction#finish() with transaction#close()
  • capture primary interactions as recipient -> donor when possible. E.g., dog eats man is primary, man eaten by dog is secondary (or inverse). Introduced to remove burden of flipping interactions on ingesting data from GloBI.

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • increase performance when importing/parsing local datasets . When importing datasets through elton, only ~ 100 interactions per second were read. After implementing the performance fix, import throughput was observed to be in the order of 10k interactions per second.

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

Improvements

Bug fixes

  • ensure proper line endings in nquad export

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • set client passive mode on ftp handler to avoid firewall issues
  • populate reference citation and url for dwca using dc:references

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

  • ensure that neo4j dataset populates citations properly

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • add more term mappings for DwC-A importer

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

Improvements

  • add interaction mappings for web-of-life
  • various logging improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • enable arthropodEasyCapture parser for streaming
  • inherit arthropodEasyCapture citations for underlying resources
  • improve datetime parsing for Bell 2015

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • mores updates to data import sequence to favor data streaming in Elton
  • cache CMECS classification in GoMexSI importer
  • account for varying date formats in GoMexSI

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • update data import sequence to favor data streaming in Elton
  • index GoMexSI event dates

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • make CMECS resolver a little more lenient
  • update taxon-graph version
  • make GoMexSI parser log instead of throw of number parsing
  • add mapping for GBIF from https://www.gbif.org/species/

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 6 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • make DOI resolver min match score configurable; allow DOI cache to be explicitly initialized.

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

  • implement retry strategy for http result code 429, too many requests
  • refactor doi resolver into separate module; make min match score configurable;
  • decouple normalizer from globalnames service; move globalnames service into nomer

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

n/a

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 7 years ago

Global Biotic Interactions -

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 7 years ago

Global Biotic Interactions -

Features

  • make max links to taxa configurable. This is used when resolving taxa from a taxon cache.

Improvements

  • various improvements related to Avian Diet Database support - custom mapping of habitat terms, populate location information and cleanup citation strings.
  • add body part mapping support for table imports
  • remove suspicious name matches introduced related to https://github.com/GlobalNamesArchitecture/gni/issues/48 .
  • add geonames prefix expansion support ( suggested by @tkuhn )

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 7 years ago

Global Biotic Interactions -

Features

  • make max links to taxa configurable. This is used when resolving taxa from a taxon cache.

Improvements

  • improve name matching throughput by setting reasonable default for max links to taxa

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 7 years ago

Global Biotic Interactions - dataset import performance, wikidata id support

Features

  • add support for wikidata id shorthand

Improvements

  • improve dataset import performance by reducing usage of expensive datetime parsing

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 7 years ago

Global Biotic Interactions -

Features

Improvements

  • Improve performance by removing ordering of results by frequency of occurence
  • Replace http prefixes by https for eol media images in order to prevent insecure image in secure pages
  • move term matchers into Nomer project at https://github.com/globalbioticinteractions/nomer .
  • upgrade to crossref api v2.0 ; only include only DOIs found by citation with match score > 50 to reduce false positives (see #338).

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 7 years ago

Global Biotic Interactions -

Features

  • Separate dynamic name correcting / matching / resolving from building neo4j search index. Instead use released taxon cache/map to resolve and link names (taxon, ontological term). Dynamic name resolving will be done through https://github.com/globalbioticinteractions/nomer , a dedicated name matching tool that produces taxon cache/maps.

Improvements

  • Improve performance of wide taxonomic queries (e.g., Animalia interacts with Animalia, see #330)

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

Improvements

Bug fixes

  • Ignore non numeric ITIS ids in Hurlbert dataset
  • Use source names if database names are missing in GoMexSI data
  • Update taxon url scheme for links to SeaLifeBase

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

  1. First pass at supporting GlobalWeb: an online collection of food webs https://www.globalwebdb.com (see https://github.com/jhpoelen/eol-globi-data/issues/322)

Improvements

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

  1. First pass at supporting Nordic Saproxylic Database format (see https://github.com/jhpoelen/eol-globi-data/issues/320)

Improvements

  1. Support ITIS taxon ids in Hurlbert Avian Diet Data (see https://github.com/hurlbertlab/dietdatabase/issues/83).
  2. Include source code in maven artifacts releases .
  3. Populate last accessed at time stamp from dataset configuration instead of system time.
  4. Easier access to citation tsv .
  5. Make cypher endpoint configurable in web api.

Bug fixes

  1. make reference citation unique in dataset context

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

  1. Switch to using offline cache created by https://github.com/globalbioticinteractions/elton to compile neo4j graph from datasets .

Improvements

Bug fixes

  1. properly handle gzipped resources inside cached dataset archive zip files

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

Improvements

  1. replaced customized importer for https://github.com/EOL/pseudonitzchia with meta-table-based configuration. See https://github.com/globalbioticinteractions/pseudonitzchia for (temporary) example configuration.
  2. enable caching for resources associated with Raymond, B., Marshall, M., Nevitt, G., Gillies, C., van den Hoff, J., Stark, J.S., Losekoot, M., Woehler, E.J., and Constable, A.J. (2011) A Southern Ocean dietary database. Ecology 92(5):1188. Available from http://dx.doi.org/10.1890/10-1907.1

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

Features

Improvements

  1. ignore fields with undefined columns rather than crashing on importing of datasets with external data table definitions (e.g., https://github.com/globalbioticinteractions/natural-history-museum-london-interactions-bank and https://github.com/globalbioticinteractions/natural-history-museum-london-interactions-bank/issues/4). Whenever number of columns in data is greater than the number of defined columns, a warning is logged.

Bug fixes

  1. fix bug that prevented json-ld dataset (e.g., https://github.com/globalbioticinteractions/jsonld-template-dataset) from being imported.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fixing a bug that prevented some datasets from being imported due to a resource mapping issue.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. support content-based caching of dataset resources to increase reproducibility and stability. Dataset resources include GloBI enabled github/zenodo repositories. Also, the resources include data files or web api responses that are used to extract species interaction data. Local directories are used to package all the source data related to a particular dataset such that a data import can be replayed at some later point in time without having to assume that the associated web servers are still on-line.

For example - a NOAA REEM dataset available at https://zenodo.org/record/229505/files/globalbioticinteractions/noaa-reem-v0.1.zip would result in a local directory that contains something like:

/datasets/globalbioticinteractions/noaa-reem/access.tsv
/datasets/globalbioticinteractions/noaa-reem/13d87c0609080b2fbf527a959fca260e9401f772fd8ee65952a487bce39712e1
/datasets/globalbioticinteractions/noaa-reem/2cf36a75c21fe96e5b73f67a581d21d0eb69c5beb5092c0a7820266b03448731
/datasets/globalbioticinteractions/noaa-reem/660ba0ddebf9c8e7dcd20a77ea3ce26d9a6e3a67a046336880f8de9e94899f5d
/datasets/globalbioticinteractions/noaa-reem/6bd280454f0e6ab2388e87a78e459cedc0e2af34dbfeb9184aa9c0a653950ae4
/datasets/globalbioticinteractions/noaa-reem/8825692b70bd6262bc4e43cb46e2711443047d16c6c4d8806c5e463f31881ee8
/datasets/globalbioticinteractions/noaa-reem/d6cb297d8066ef57088b8fcc793203ad05ec434e7255e6e201fcb90cc6352270

Where the access.tsv file contains the relations between the web uris, associated cache filenames (e.g., d6cb297d...) and access time/date. The associated local files names are generated from the content of the resources using SHA2/SHA256.

dataset name resource uri local filename/content-hash accessed at type
globalbioticinteractions/noaa-reem https://zenodo.org/record/229505/files/globalbioticinteractions/noaa-reem-v0.1.zip   2017-09-16T05:57:20Z application/globi
globalbioticinteractions/noaa-reem https://zenodo.org/record/229505/files/globalbioticinteractions/noaa-reem-v0.1.zip 13d87c0609080b2fbf527a959fca260e9401f772fd8ee65952a487bce39712e1 2017-09-16T05:57:20Z
... ... ... ... ...
globalbioticinteractions/noaa-reem http://access.afsc.noaa.gov/REEM/WebDietData/showdata5.php?NODC=1&Region=BS 8825692b70bd6262bc4e43cb46e2711443047d16c6c4d8806c5e463f31881ee8 2017-09-16T05:58:28Z  
globalbioticinteractions/noaa-reem http://access.afsc.noaa.gov/REEM/WebDietData/showdata5.php?NODC=1&Region=GOA 2cf36a75c21fe96e5b73f67a581d21d0eb69c5beb5092c0a7820266b03448731 2017-09-16T05:58:55Z  

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fix tsv export bug (see #311)
  2. more verbose logging on importing interactions (e.g., https://github.com/globalbioticinteractions/natural-history-museum-london-interactions-bank/issues/3)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 7 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. zenodo integration improvements #283
  2. improved dataset reports and api access (e.g. #281)
  3. integration maintenance of various kinds: web-of-life, fishbase/sealifebase, Atlas of Living Australia, National Biodiversity Network and more.
  4. improvement to tsv export format: include all taxon ids across various linked taxonomies
  5. some initial usage of nanopubs, trusty uris (see #291)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. first pass as support for ingesting http://fishbase.org and http://sealifebase.org diet, fooditems, and predator records (see #179)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. cleanup temporary files related to taxon lookup services (see #278)
  2. minor improvements to importer for http://bioinfo.org.uk
  3. replace tabs with whitespaces when exporting text in tsv files
  4. dataset checker tool (github tool) now logs warnings/errors after run, making for a bit more aligned and hopefully easier to inspect report

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fixes in support for the hurlbert dataset format (see #276)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. optimizing resolving DOI for citations a cache
  2. adding support for hurlbert and thessen dataset format (see https://github.com/hurlbertlab/dietdatabase/issues/40) for github auto-discovery
  3. allowing searches by datasets / namespaces through web api

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. ensuring that akin data importer uses dataset context to load resources
  2. allowing to disable/enable resolving of references (citation --> doi) using globi.json
  3. renaming "said" format to "siad" to reflect acronym for Species Interaction of Australia Database.
  4. introducing experimental data source reporting api endpoint, allowing for retrieving statistics by source id path to support features like showing taxonomic name match percentage for data source (see #273)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fix mapping of repository format --> importer, allowing spire and baremore to import using a suitable importer
  2. ensure that software version is printed when starting command line tools.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. move previously embedded dataset out to individual github repositories
  2. bug fix in cached dataset resource loading
  3. make inaturalist interaction type mapping resource relative to dataset archive

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. enabling federation of previously static data sources by loading resources through dataset context

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fix issue in Zenodo integration that caused only one published dataset to be seen, leaving GloBI unaware of published, citable, datasets.
  2. expand list of defined data source types/formats that may be used for GitHub-based datasets.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions - Decouple GitHub checker from GitHub API

This maintenance release includes, but is not limited to:

  1. decoupling GitHub Checker tool from using the GitHub api to avoid build failures due to exceeding api rate limits.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions - Add Logging to GitHub Checker Tool

This maintenance release includes, but is not limited to:

  1. adding more log message to GitHub Checker tool to enable for more detailed troubleshooting of datasets / parsers.
  2. ensuring that GitHub Checker Tool restricts the number of info, warning and error message to 500 to avoid flooding of travis log files.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions - fixes to GitHub Checker Tool

This maintenance release includes, but is not limited to:

  1. ensuring that GitHub Checker Tool fails if an unexpected exceptions occur during the import validation process
  2. releasing memory for Seltmann / Coetzer importers in an effort to avoid out of memory exceptions on resource constrained travis containers.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions - Simplify GitHub Data Repository Checker Tool

This maintenance release includes, but is not limited to:

  1. a simplification of the github data repo checker tool. previously, the tool attempted to resolve names, citations, and ecoregions. Now, it just counts the number of interactions. The tool is used for running automated sanity checks on travis-ci.org like https://travis-ci.org/globalbioticinteractions/template-dataset . See https://github.com/globalbioticinteractions/template-dataset/blob/master/.travis.yml for example of travis configuration.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions - zenodo support

This maintenance release includes, but is not limited to:

  1. support for github data repositories, published through Zenodo (https://github.com/jhpoelen/eol-globi-data/issues/212).
  2. support for interaction data expressed in specific taxonomy (https://github.com/jhpoelen/eol-globi-data/issues/252 and https://github.com/jhpoelen/eol-globi-data/issues/253)
  3. integrate with global names parser (https://github.com/jhpoelen/eol-globi-data/issues/155)
  4. publish flat tsv files to easy parsing and grepping (https://github.com/jhpoelen/eol-globi-data/issues/235)
  5. travis integration for individual datasets (https://github.com/jhpoelen/eol-globi-data/issues/228)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 8 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. fix related to support for relative schema urls related to experimental support for https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/ .

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 9 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. update to GitHub repository verification tool (see https://github.com/jhpoelen/eol-globi-data/issues/228)
  2. update to NCBI LinkOut url descriptors
  3. include support for relative schema urls related to experimental support for https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/ .

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 9 years ago

Global Biotic Interactions -

This maintenance release includes, but is not limited to:

  1. externalized iNaturalist interaction mappings (https://github.com/jhpoelen/eol-globi-data/issues/189)
  2. various new datasets and related parsers (e.g. https://github.com/jhpoelen/eol-globi-data/issues/210 https://github.com/jhpoelen/eol-globi-data/issues/193 https://github.com/jhpoelen/eol-globi-data/issues/216)
  3. sitemap generation
  4. generation of NCBI LinkOut resource files
  5. preliminary support for w3c meta-tables (e.g. https://github.com/globalbioticinteractions/noaa-reem and https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/)
  6. creation of GitHub repository verification tool (see https://github.com/jhpoelen/eol-globi-data/issues/228)
  7. various bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen almost 9 years ago

Global Biotic Interactions - new inaturalist interaction mappings; seltmann importer update

This maintenance release includes:

  1. new iNaturalist interaction mappings
  2. update to Seltmann importer (e.g. Digital Bees, Tri-trophic Network)
  3. disable test for http://kelpforest.ucsc.edu (not reachable, contacted author)

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - introducing kills/killedBy; new iNaturalist interaction mapping; common names from WoRMS; allow GitHub tsv import with taxon id only

This maintenance release includes:

  1. new iNaturalist interaction mappings
  2. new kills/killedBy interaction types
  3. allow github TSV interaction records without taxon name, but with taxon id
  4. support common names (vernaculars) from World Register of Marine Species (WoRMS) taxonomy

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - inaturalist integ improvement; mappings for plastic material; direct ncbi taxon integration

This maintenance release includes:

  1. improvement to iNaturalist integration 0ff5e5afca2b77e90e6674fb503295aaf5ad6fd6 https://github.com/inaturalist/inaturalist/issues/733
  2. direct integration with NCBI taxonomy to side-step performance issue 309064222870631c4bf293fe12ce9574b18364ab https://github.com/EOL/tramea/issues/24 https://github.com/jhpoelen/eol-globi-data/issues/145
  3. add plastic material mapping for GoMexSI prey items b58bd702aa258610a031bb32421b0714c22847b0

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - re-enable term mapping such as life stages

Includes a blocking bug fix in v0.7.2 that prevented the mapping of life stage terms.

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - interaction mapping updates; fishbase integration prototype; bugfixes; taxon name resolution refactoring

This release include minor bug fixes and updates such as:

  1. Add source citation (e.g. Bell et al. 2015 0ee435c4351a14ebdf9ede12e23c10ae265a5a9e )
  2. fix or improve interaction mappings (e.g. inaturalist e10d46d73ca25d7b0966f6c9e9c3bc22d16937dc , bioinfo 09ee59b8e070b549d3c7297df754e6f4be4ce1cc)
  3. first step towards extracting taxon name resolution code from data-tool module 41d495a95298f5cee715e9bf055f84588f297dad in preparation of improving performance of taxon resolution #145
  4. a first prototype of integrating with fishbase (not available yet!) using https://github.com/ropensci/fishbaseapi #179

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - add inaturalist mapping; remove roll-up interaction archive

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago

Global Biotic Interactions - a second initial release

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen over 9 years ago