20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration

Biodiversity information is made available through numerous databases that each have their own data models, web services, and data types. Combining data across databases leads to new insights, but is not easy because each database uses its own system of identifiers. In the absence of stable and interoperable identifiers, databases are often linked using taxonomic names. This labor intensive, error prone, and lengthy process relies on accessible versions of nomenclatural authorities and fuzzy-matching algorithms. To approach the challenge of linking diverse data, more than technology is needed. New social collaborations like the Global Unified Open Data Architecture (GUODA) that combines skills from diverse groups of computer engineers from iDigBio, server resources from the Advanced Computing and Information Systems (ACIS) Lab, global-scale data presentation from EOL, and independent developers and researchers are what is needed to make concrete progress on finding relationships between biodiversity datasets. This paper will discuss a technical solution developed by the GUODA collaboration for faster linking across databases with a use case linking Wikidata and the Global Biotic Interactions database (GloBI). The GUODA infrastructure is a 12-node, high performance computing cluster made up of about 192 threads with 12 TB of storage and 288 GB memory. Using GUODA, 20 GB of compressed JSON from Wikidata was processed and linked to GloBI in about 10–11 min. Instead of comparing name strings or relying on a single identifier, Wikidata and GloBI were linked by comparing graphs of biodiversity identifiers external to each system. This method resulted in adding 119,957 Wikidata links in GloBI, an increase of 13.7% of all outgoing name links in GloBI. Wikidata and GloBI were compared to Open Tree of Life Reference Taxonomy to examine consistency and coverage. The process of parsing Wikidata, Open Tree of Life Reference Taxonomy and GloBI archives and calculating consistency metrics was done in minutes on the GUODA platform. As a model collaboration, GUODA has the potential to revolutionize biodiversity science by bringing diverse technically minded people together with high performance computing resources that are accessible from a laptop or desktop. However, participating in such a collaboration still requires basic programming skills

20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration

Biodiversity information is made available through numerous databases that each have their own data models, web services, and data types. Combining data across databases leads to new insights, but is not easy because each database uses its own system of identifiers. In the absence of stable and interoperable identifiers, databases are often linked using taxonomic names. This labor intensive, error prone, and lengthy process relies on accessible versions of nomenclatural authorities and fuzzy-matching algorithms. To approach the challenge of linking diverse data, more than technology is needed. New social collaborations like the Global Unified Open Data Architecture (GUODA) that combines skills from diverse groups of computer engineers from iDigBio, server resources from the Advanced Computing and Information Systems (ACIS) Lab, global-scale data presentation from EOL, and independent developers and researchers are what is needed to make concrete progress on finding relationships between biodiversity datasets. This paper will discuss a technical solution developed by the GUODA collaboration for faster linking across databases with a use case linking Wikidata and the Global Biotic Interactions database (GloBI). The GUODA infrastructure is a 12-node, high performance computing cluster made up of about 192 threads with 12 TB of storage and 288 GB memory. Using GUODA, 20 GB of compressed JSON from Wikidata was processed and linked to GloBI in about 10 - 11 min. Instead of comparing name strings or relying on a single identifier, Wikidata and GloBI were linked by comparing graphs of biodiversity identifiers external to each system. This method resulted in adding 119,957 Wikidata links in GloBI, an increase of 13.7% of all outgoing name links in GloBI. Wikidata and GloBI were compared to Open Tree of Life Reference Taxonomy to examine consistency and coverage. The process of parsing Wikidata, Open Tree of Life Reference Taxonomy and GloBI archives and calculating consistency metrics was done in minutes on the GUODA platform. As a model collaboration, GUODA has the potential to revolutionize biodiversity science by bringing diverse technically minded people together with high performance computing resources that are accessible from a laptop or desktop. However, participating in such a collaboration still requires basic programming skills

Liberating host–virus knowledge from biological dark data

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host–pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.info:eu-repo/semantics/publishedVersio

Open Science Principles for Accelerating Trait-Based Science Across the Tree of Life

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles—open data, open source and open methods—is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Global Biotic Interactions: Benefits of Pragmatic Reuse of Species Interaction Datasets

Slides of Seminar at Leibniz Institute for Zoo and Wildlife Research Berlin, Germany on 9 January 2020

Global Biotic Interactions: Taxon Graph

<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p><p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p><p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p><p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p><p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p><p>Files<br>  <br>  README <br>      this file</p><p>  taxonCache.tsv.gz <br>     Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br>  taxonCache.tsv.sha256<br>     sha256 hash of taxonCache.tsv</p><p>  taxonCacheFirst10.tsv<br>      Header and 10 following lines from taxonCache.tsv</p><p>  taxonCacheFirst10.tsv.sha256<br>      sha256 hash of taxonCacheFirst10.tsv<br>       <br>  taxonMap.tsv.gz <br>      Links between taxon name and ids across various taxon providers. </p><p>  taxonMap.tsv.sha256 <br>      sha256 hash of taxonMap.tsv</p><p>  taxonMapFirst10.tsv<br>      Header and 10 following lines from taxonMap.tsv<br> <br>  taxonMapFirst10.tsv.sha256<br>      sha256 hash of taxonMapFirst10.tsv</p><p>  prefixes.tsv<br>      Term prefixes and their associated uri schemes. </p><p>  names.tsv.gz<br>      Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p><p>  names.tsv.sha256<br>      sha256 hash of names.tsv</p><p>  namesUnresolved.tsv.gz<br>      Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p><p>  namesUnresolved.tsv.sha256<br>      sha256 hash of namesUnresolved.tsv </p><p>Column Descriptions</p><p>  taxonCache.tsv.gz </p><p>    1 | id<br>    2 | name<br>    3 | rank<br>    4 | commonNames<br>    5 | path<br>    6 | pathIds <br>    7 | pathNames<br>    8 | externalUrl<br>    9 | thumbnailUrl<br> <br>  taxonMap.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName<br>    3 | resolvedTaxonId<br>    4 | resolvedTaxonName</p><p>  names.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>   namesUnresolved.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>References</p><p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p><p>Updates</p><p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p><p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p><p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p><p>This taxon archive version includes the following:</p><p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p><p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p><p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p><p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p><p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p><p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p><p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p><p>This taxon archive version includes the following:</p><p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p><p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p><p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p><p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p><p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p><p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p><p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p><p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p><p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p><p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p><p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p><p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p><p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura" | grep -v -P "Gamarus" |  grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p><p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p><p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p><p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p><p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p><p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p><p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p><p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p><p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p><p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p><p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p><p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p><p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p><p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p><p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p><p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p><ol><li>update taxon graph build script to fit into existing taxonMap/taxonCache schema</li><li>fix various bugs</li><li>remove internal validation until a more up-to-date validation method is available</li></ol><p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-24</p><ol><li>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</li></ol><p>org.globalbioticinteractions.taxon v0.4.3, 2022-10-26</p><ol><li>apply patch 20231026-01 to address https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p>org.globalbioticinteractions.taxon v0.4.4, 2022-10-26</p><ol><li>apply patch 20231026-02 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p>org.globalbioticinteractions.taxon v0.4.5, 2022-10-26</p><ol><li>apply patch 20231026-03 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p> </p><p> </p><p> </p&gt

Global Biotic Interactions: Taxon Graph

<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p><p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p><p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p><p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p><p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p><p>Files<br>  <br>  README <br>      this file</p><p>  taxonCache.tsv.gz <br>     Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br>  taxonCache.tsv.sha256<br>     sha256 hash of taxonCache.tsv</p><p>  taxonCacheFirst10.tsv<br>      Header and 10 following lines from taxonCache.tsv</p><p>  taxonCacheFirst10.tsv.sha256<br>      sha256 hash of taxonCacheFirst10.tsv<br>       <br>  taxonMap.tsv.gz <br>      Links between taxon name and ids across various taxon providers. </p><p>  taxonMap.tsv.sha256 <br>      sha256 hash of taxonMap.tsv</p><p>  taxonMapFirst10.tsv<br>      Header and 10 following lines from taxonMap.tsv<br> <br>  taxonMapFirst10.tsv.sha256<br>      sha256 hash of taxonMapFirst10.tsv</p><p>  prefixes.tsv<br>      Term prefixes and their associated uri schemes. </p><p>  names.tsv.gz<br>      Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p><p>  names.tsv.sha256<br>      sha256 hash of names.tsv</p><p>  namesUnresolved.tsv.gz<br>      Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p><p>  namesUnresolved.tsv.sha256<br>      sha256 hash of namesUnresolved.tsv </p><p>Column Descriptions</p><p>  taxonCache.tsv.gz </p><p>    1 | id<br>    2 | name<br>    3 | rank<br>    4 | commonNames<br>    5 | path<br>    6 | pathIds <br>    7 | pathNames<br>    8 | externalUrl<br>    9 | thumbnailUrl<br> <br>  taxonMap.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName<br>    3 | resolvedTaxonId<br>    4 | resolvedTaxonName</p><p>  names.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>   namesUnresolved.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>References</p><p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p><p>Updates</p><p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p><p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p><p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p><p>This taxon archive version includes the following:</p><p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p><p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p><p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p><p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p><p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p><p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p><p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p><p>This taxon archive version includes the following:</p><p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p><p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p><p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p><p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p><p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p><p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p><p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p><p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p><p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p><p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p><p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p><p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p><p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura" | grep -v -P "Gamarus" |  grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p><p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p><p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p><p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p><p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p><p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p><p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p><p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p><p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p><p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p><p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p><p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p><p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p><p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p><p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p><p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p><ol><li>update taxon graph build script to fit into existing taxonMap/taxonCache schema</li><li>fix various bugs</li><li>remove internal validation until a more up-to-date validation method is available</li></ol><p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-24</p><ol><li>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</li></ol><p>org.globalbioticinteractions.taxon v0.4.3, 2022-10-26</p><ol><li>apply patch 20231026-01 to address https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p> </p><p> </p><p> </p&gt

Global Biotic Interactions: Taxon Graph

<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p><p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p><p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p><p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p><p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p><p>Files<br>  <br>  README <br>      this file</p><p>  taxonCache.tsv.gz <br>     Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br>  taxonCache.tsv.sha256<br>     sha256 hash of taxonCache.tsv</p><p>  taxonCacheFirst10.tsv<br>      Header and 10 following lines from taxonCache.tsv</p><p>  taxonCacheFirst10.tsv.sha256<br>      sha256 hash of taxonCacheFirst10.tsv<br>       <br>  taxonMap.tsv.gz <br>      Links between taxon name and ids across various taxon providers. </p><p>  taxonMap.tsv.sha256 <br>      sha256 hash of taxonMap.tsv</p><p>  taxonMapFirst10.tsv<br>      Header and 10 following lines from taxonMap.tsv<br> <br>  taxonMapFirst10.tsv.sha256<br>      sha256 hash of taxonMapFirst10.tsv</p><p>  prefixes.tsv<br>      Term prefixes and their associated uri schemes. </p><p>  names.tsv.gz<br>      Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p><p>  names.tsv.sha256<br>      sha256 hash of names.tsv</p><p>  namesUnresolved.tsv.gz<br>      Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p><p>  namesUnresolved.tsv.sha256<br>      sha256 hash of namesUnresolved.tsv </p><p>Column Descriptions</p><p>  taxonCache.tsv.gz </p><p>    1 | id<br>    2 | name<br>    3 | rank<br>    4 | commonNames<br>    5 | path<br>    6 | pathIds <br>    7 | pathNames<br>    8 | externalUrl<br>    9 | thumbnailUrl<br> <br>  taxonMap.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName<br>    3 | resolvedTaxonId<br>    4 | resolvedTaxonName</p><p>  names.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>   namesUnresolved.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>References</p><p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p><p>Updates</p><p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p><p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p><p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p><p>This taxon archive version includes the following:</p><p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p><p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p><p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p><p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p><p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p><p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p><p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p><p>This taxon archive version includes the following:</p><p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p><p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p><p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p><p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p><p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p><p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p><p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p><p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p><p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p><p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p><p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p><p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p><p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura" | grep -v -P "Gamarus" |  grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p><p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p><p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p><p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p><p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p><p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p><p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p><p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p><p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p><p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p><p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p><p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p><p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p><p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p><p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p><p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p><ol><li>update taxon graph build script to fit into existing taxonMap/taxonCache schema</li><li>fix various bugs</li><li>remove internal validation until a more up-to-date validation method is available</li></ol><p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-24</p><ol><li>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</li></ol><p> </p><p> </p&gt

Global Biotic Interactions: Taxon Graph

<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p><p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p><p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p><p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p><p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p><p>Files<br>  <br>  README <br>      this file</p><p>  taxonCache.tsv.gz <br>     Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br>  taxonCache.tsv.sha256<br>     sha256 hash of taxonCache.tsv</p><p>  taxonCacheFirst10.tsv<br>      Header and 10 following lines from taxonCache.tsv</p><p>  taxonCacheFirst10.tsv.sha256<br>      sha256 hash of taxonCacheFirst10.tsv<br>       <br>  taxonMap.tsv.gz <br>      Links between taxon name and ids across various taxon providers. </p><p>  taxonMap.tsv.sha256 <br>      sha256 hash of taxonMap.tsv</p><p>  taxonMapFirst10.tsv<br>      Header and 10 following lines from taxonMap.tsv<br> <br>  taxonMapFirst10.tsv.sha256<br>      sha256 hash of taxonMapFirst10.tsv</p><p>  prefixes.tsv<br>      Term prefixes and their associated uri schemes. </p><p>  names.tsv.gz<br>      Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p><p>  names.tsv.sha256<br>      sha256 hash of names.tsv</p><p>  namesUnresolved.tsv.gz<br>      Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p><p>  namesUnresolved.tsv.sha256<br>      sha256 hash of namesUnresolved.tsv </p><p>Column Descriptions</p><p>  taxonCache.tsv.gz </p><p>    1 | id<br>    2 | name<br>    3 | rank<br>    4 | commonNames<br>    5 | path<br>    6 | pathIds <br>    7 | pathNames<br>    8 | externalUrl<br>    9 | thumbnailUrl<br> <br>  taxonMap.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName<br>    3 | resolvedTaxonId<br>    4 | resolvedTaxonName</p><p>  names.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>   namesUnresolved.tsv.gz</p><p>    1 | providedTaxonId<br>    2 | providedTaxonName</p><p>References</p><p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p><p>Updates</p><p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p><p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p><p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p><p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p><p>This taxon archive version includes the following:</p><p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p><p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p><p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p><p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p><p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p><p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p><p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p><p>This taxon archive version includes the following:</p><p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p><p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p><p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p><p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p><p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p><p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p><p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p><p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p><p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p><p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p><p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p><p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p><p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p><p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p><p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura" | grep -v -P "Gamarus" |  grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p><p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p><p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p><p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p><p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p><p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p><p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p><p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p><p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p><p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p><p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p><p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p><p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p><p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p><p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p><p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p><p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p><p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p><p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p><ol><li>update taxon graph build script to fit into existing taxonMap/taxonCache schema</li><li>fix various bugs</li><li>remove internal validation until a more up-to-date validation method is available</li></ol><p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-24</p><ol><li>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</li></ol><p>org.globalbioticinteractions.taxon v0.4.3, 2022-10-26</p><ol><li>apply patch 20231026-01 to address https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p>org.globalbioticinteractions.taxon v0.4.4, 2022-10-26</p><ol><li>apply patch 20231026-02 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</li></ol><p> </p><p> </p><p> </p&gt