mdoering

In this 2021-03-03 edition of the GBIF Backbone we have adressed various issues both in content but also in development work that lead to a better overall taxonomy. Further details can be seen in the closed Github project board. Here we want to point out some major achievements:

Data source changes

We have advanced the Backbone Building so that we can block certain groups or subtree of a source by configuration only. This new feature has been used to block the prokaryotic kingdoms Bacteria and Archaea as well as the Fabaceae plant family from Catalogue of Life.

Instead we decided to follow Kews World Checklist of Vascular Plants for Fabaceae, which we made available in Darwin Core to index into GBIF.

mdoering

mdoering

[
  {"id":"5E7FB","name":"Aves","rank":"class","code":"zoological","status":"accepted","children":[
    {"id":"5CY9X","name":"Accipitriformes","rank":"order","code":"zoological","status":"accepted","children":[
      {"id":"5D73B","name":"Accipitridae","authorship":"Vigors, 1824","rank":"family","code":"zoological","status":"accepted","children":[
        {"id":"5REGP","name":"Accipitrinae","rank":"subfamily","code":"zoological","status":"synonym","children":[]},
        {"id":"5DXFV","name":"Accipiter","authorship":"Brisson, 1760","rank":"genus","code":"zoological","status":"accepted","children":[
          {"id":"5E9DM","name":"Accipiter albogularis","authorship":"G. R. Gray, 1870","rank":"species","code":"zoological","status":"accepted","children":[
            {"id":"5ELB7","name":"Accipiter albogularis albogularis","authorship":"G. R. Gray, 1870","rank":"subspecies","code":"zoological","status":"accepted","children":[]},
            {"id":"5ELB6","name":"Accipiter albogularis eichhorni","authorship":"Har

mdoering

COL RELEASE
2230: Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P. M., Bourgoin T., DeWalt R. E., Decock W., van Nieukerken E. J., Penev L. (eds.) (2020). Species 2000 & ITIS Catalogue of Life, 3rd November 2020. Digital resource at www.catalogueoflife.org. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858.

SOURCES:
1005: Oosterbroek P. (2020). CCW: Catalogue of Craneflies of the World (version Jul 2013). In: Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P. M., Bourgoin T., DeWalt R. E., Decock W., van Nieukerken E. J., Penev L. (eds.) (2020). Species 2000 & ITIS Catalogue of Life, 3rd November 2020. Digital resource at www.catalogueoflife.org. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858.
1006: Vignes-Lebbe R., Gallut C. (2020). CIPA: Computer Aided Identification of Phlebotomine sandflies of Americas (version 3, Mar 2011). In: Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P. M., Bourgoin T., DeWalt R. E., Decock W., van Nieukerken

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Animalia [kingdom]
  Acanthocephala [phylum]
    Archiacanthocephala [class]
      Apororhynchida [order]
        Apororhynchidae [family]
      Gigantorhynchida [order]
        Giganthorhynchidae [family]
      Moniliformida [order]
        Moniliformidae [family]
      Oligacanthorhynchida [order]

mdoering

MAC
 table_name  | row_estimate | total_bytes | index_bytes | toast_bytes | table_bytes | total  |  index  |   toast    | table  
-------------+--------------+-------------+-------------+-------------+-------------+--------+---------+------------+--------
 test-int4   |        5e+06 |   323534848 |   142221312 |        8192 |   181305344 | 309 MB | 136 MB  | 8192 bytes | 173 MB
 test-int2   |        5e+06 |   323993600 |   142680064 |        8192 |   181305344 | 309 MB | 136 MB  | 8192 bytes | 173 MB
 test-enum   |        5e+06 |   293650432 |   112336896 |        8192 |   181305344 | 280 MB | 107 MB  | 8192 bytes | 173 MB
 test-int4[] |  4.99999e+06 |   306806784 |     5505024 |        8192 |   301293568 | 293 MB | 5376 kB | 8192 bytes | 287 MB
 test-int2[] |  4.99999e+06 |   266493952 |     5505024 |        8192 |   260980736 | 254 MB | 5376 kB | 8192 bytes | 249 MB
 test-enum[] |  4.99998e+06 |   346955776 |     5505024 |        8192 |   341442560 | 331 MB | 5376 kB | 8192 bytes | 326 MB

mdoering

-- ALL GENUS HOMONYMS
WITH homs AS (
 SELECT u.rank, n.canonical_name
 FROM name_usage u JOIN name n ON u.name_fk = n.id
 WHERE u.dataset_key = nubkey() AND u.deleted IS NULL AND NOT u.is_synonym AND u.rank='GENUS'::rank
 GROUP BY u.rank, n.canonical_name
 HAVING count(*) > 1
) 
SELECT u.id, n.canonical_name, u.rank, n.scientific_name, u.is_synonym, u.status,
    u.kingdom_fk, u.phylum_fk, u.class_fk, u.order_fk, u.family_fk, u.genus_fk

mdoering

-- GENUS HOMONYMS WITH THE SAME CLASSIFICATION, ALL DOUBTFUL AND AT LEAST ONE MISSING AUTHORSHIP
-- BUT RETURNING ALL USAGES WITHIN THAT KINGDOM WITH THAT NAME REGARDLESS THEIR CLASSIFICATION
WITH homs AS (
 SELECT u.rank, n.canonical_name, u.kingdom_fk, u.phylum_fk, u.class_fk, u.order_fk, u.family_fk
 FROM name_usage u JOIN name n ON u.name_fk = n.id
 WHERE u.dataset_key = nubkey() AND u.deleted IS NULL AND NOT u.is_synonym AND u.rank='GENUS'::rank 
 GROUP BY u.rank, n.canonical_name, u.kingdom_fk, u.phylum_fk, u.class_fk, u.order_fk, u.family_fk
 HAVING count(*) > 1 AND count(distinct status)=1 AND bool_or(n.canonical_name=n.scientific_name) 
) 

mdoering

// 20190903122905
// http://localhost:8080/dataset/3/tree/f55812e8-5422-402e-b071-b67a9cdf481f--incertae-sedis--FAMILY

[
  {
    "datasetKey": 3,
    "id": "f55812e8-5422-402e-b071-b67a9cdf481f",
    "parentId": "0",
    "name": "<i>Viruses</i>",
    "rank": "kingdom",