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Source for the DiSSCoUK Data Portal provided by GBIF Hosted Portals
https://dissco-uk.org/
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Specimens from UK institutions not appearing on data portal #5

Closed TaraWainwright closed 1 year ago

TaraWainwright commented 2 years ago

The specimen data portal (https://uk-collections.hp.gbif-staging.org/specimen/search) is excluding specimens from UK institutions that are publishing to GBIF but don't have a GRSciColl entry.

It seems the specimens are being filtered by GRSciColl and not just whether the specimens are from UK institutions.

E.g., the Botanical Society of Britain and Ireland have uploaded the specimen Rubus anisacanthos but when this specimen is searched on the portal, only NHM specimens are shown: Screenshot (94) Screenshot (93)

The list of publishing institutions not on GRSciColl:

MortenHofft commented 2 years ago

Indeed it does. That is intentional. But you control the scope. https://github.com/gbif/hp-uk-collections/blob/master/_includes/js/config.js#L59 Currently it has to be published by a UK publisher and has to be matched to a grscicoll entry (institution OR collection).

This was, as I understood it, what we agreed in our initial meeting. Well knowing that it would require cleaning data: that is

Not doing so would create an odd inconsistency with the institution and collection pages I think. So I would recommend getting the GrSciColl entries fixed instead. Let me know if I can help with anything

lmfrench commented 2 years ago

Thanks yes this is fine, we just wanted to make sure we knew how it was working! Will close this issue, and we will contact the organisations listed above

MortenHofft commented 2 years ago

Will it help if I compile a list of publishers/datasets that have specimens that do NOT match to GrSciColl entries?

lmfrench commented 2 years ago

We think the list above are the UK publishers with specimens that have no GrSciColl entry - it would be great if you are able to check and let us know if we have missed anyone

MortenHofft commented 2 years ago

Using GraphQL with query

# give me top 1000 datasets that math the filter
query table($predicate: Predicate, $size: Int = 20, $from: Int = 0){
  occurrenceSearch(predicate: $predicate, size: $size, from: $from) {
    facet {
      datasetKey(size: 1000) {
        key
        count
        dataset {
          title
          publishingOrganizationKey
          publishingOrganizationTitle
        }
      }
    }
  }
}

and filter (ignore Mgnify as they have 100's of datasets that do not match). Look for specimens that either have no collection OR no institution match in GrSciColl.

{
  "predicate": {
    "type": "and",
    "predicates": [
      {
        "type": "not",
        "predicate": {
          "type": "in",
          "key": "publishingOrg",
          "values": ["ab733144-7043-4e88-bd4f-fca7bf858880"]
        }
      },
      {
        "type": "or",
        "predicates": [
        {
          "type": "not",
          "predicate": {
          "type": "isNotNull",
          "key": "institutionKey"
        }
        },
        {
        "type": "not",
        "predicate": {
        "type": "isNotNull",
        "key": "collectionKey"
        }
        }
        ]
        },
      {
        "type": "in",
        "key": "basisOfRecord",
        "values": [
          "PRESERVED_SPECIMEN",
          "FOSSIL_SPECIMEN",
          "MATERIAL_SAMPLE",
          "LIVING_SPECIMEN"
        ]
      },
      {
        "type": "equals",
        "key": "publishingCountry",
        "value": "GB"
      }
    ]
  },
  "size": 50,
  "from": 0
}

I get these results

{
  "data": {
    "occurrenceSearch": {
      "facet": {
        "datasetKey": [
          {
            "key": "d8cd16ba-bb74-4420-821e-083f2bac17c2",
            "count": 4996533,
            "dataset": {
              "title": "INSDC Sequences",
              "publishingOrganizationKey": "ada9d123-ddb4-467d-8891-806ea8d94230",
              "publishingOrganizationTitle": "European Nucleotide Archive (EMBL-EBI)"
            }
          },
          {
            "key": "7e380070-f762-11e1-a439-00145eb45e9a",
            "count": 4949975,
            "dataset": {
              "title": "Natural History Museum (London) Collection Specimens",
              "publishingOrganizationKey": "19456090-b49a-11d8-abeb-b8a03c50a862",
              "publishingOrganizationTitle": "Natural History Museum"
            }
          },
          {
            "key": "6d56415d-b007-4273-9c74-bcd6b2467434",
            "count": 3543114,
            "dataset": {
              "title": "The CPR Survey",
              "publishingOrganizationKey": "f6b48504-1651-4a49-a88d-c2bc6178694d",
              "publishingOrganizationTitle": "Marine Biological Association"
            }
          },
          {
            "key": "393b8c26-e4e0-4dd0-a218-93fc074ebf4e",
            "count": 1259482,
            "dataset": {
              "title": "INSDC Host Organism Sequences",
              "publishingOrganizationKey": "ada9d123-ddb4-467d-8891-806ea8d94230",
              "publishingOrganizationTitle": "European Nucleotide Archive (EMBL-EBI)"
            }
          },
          {
            "key": "583d91fe-bbc0-4b4a-afe1-801f88263016",
            "count": 316315,
            "dataset": {
              "title": "INSDC Environment Sample Sequences",
              "publishingOrganizationKey": "ada9d123-ddb4-467d-8891-806ea8d94230",
              "publishingOrganizationTitle": "European Nucleotide Archive (EMBL-EBI)"
            }
          },
          {
            "key": "4f64e2fc-a84b-49f6-802f-e48f725717d7",
            "count": 134540,
            "dataset": {
              "title": "Manchester Museum, University of Manchester, Botany Collection",
              "publishingOrganizationKey": "b472a35a-6461-444a-a3d6-84e97e6636fe",
              "publishingOrganizationTitle": "Manchester Museum, The University of Manchester"
            }
          },
          {
            "key": "1d31211e-350e-492a-a597-34d24bbc1769",
            "count": 90634,
            "dataset": {
              "title": "Royal Botanic Gardens, Kew - Economic Botany Collection Specimens",
              "publishingOrganizationKey": "061b4f20-f241-11da-a328-b8a03c50a862",
              "publishingOrganizationTitle": "Royal Botanic Gardens, Kew"
            }
          },
          {
            "key": "cd6e21c8-9e8a-493a-8a76-fbf7862069e5",
            "count": 74715,
            "dataset": {
              "title": "Royal Botanic Gardens, Kew - Herbarium Specimens",
              "publishingOrganizationKey": "061b4f20-f241-11da-a328-b8a03c50a862",
              "publishingOrganizationTitle": "Royal Botanic Gardens, Kew"
            }
          },
          {
            "key": "717b3b87-0ebd-46b4-812b-4a29786798d9",
            "count": 65917,
            "dataset": {
              "title": "UMZC Zoological Specimens",
              "publishingOrganizationKey": "d9ccac00-9bc7-11de-a329-b8a03c50a862",
              "publishingOrganizationTitle": "The University Museum of Zoology, Cambridge"
            }
          },
          {
            "key": "33325913-c769-48ca-b7fc-1d22dfa9beee",
            "count": 58886,
            "dataset": {
              "title": "Tullie House Museum Natural History Collections",
              "publishingOrganizationKey": "72af978e-3a16-4e74-82cd-cb1d95c510fb",
              "publishingOrganizationTitle": "Cumbria Biodiversity Data Centre"
            }
          },
          {
            "key": "d740f242-6c26-4229-9a8f-b63bfab63dc6",
            "count": 58771,
            "dataset": {
              "title": "GalliForm: Galliformes occurrence records from the Indo-Malay and Palaearctic, 1800-2008",
              "publishingOrganizationKey": "2963d877-8230-45bd-a223-544376275120",
              "publishingOrganizationTitle": "Newcastle University"
            }
          },
          {
            "key": "2ecef267-0e17-4f3f-adf9-20b036e6167a",
            "count": 53895,
            "dataset": {
              "title": "Myctobase, a circumpolar database of mesopelagic fishes for new insights into deep pelagic prey fields - data",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "82d9ff5c-f762-11e1-a439-00145eb45e9a",
            "count": 52689,
            "dataset": {
              "title": "Antarctic Plant Database",
              "publishingOrganizationKey": "80420c96-95d0-44eb-9f77-339ac92051fb",
              "publishingOrganizationTitle": "UK Polar Data Centre"
            }
          },
          {
            "key": "c38cea03-d7d8-44c7-9b40-750219df831a",
            "count": 49586,
            "dataset": {
              "title": "UK abstract from Nottingham City Museums & Galleries (NCMG) Insect Collection Baseline database",
              "publishingOrganizationKey": "cd0ef235-a251-4af2-b402-a816f6a8dbcc",
              "publishingOrganizationTitle": "Nottinghamshire Biological and Geological Records Centre"
            }
          },
          {
            "key": "bba60198-3eb5-4101-954d-3e2c87df4b73",
            "count": 34140,
            "dataset": {
              "title": "Caddisfly (Trichoptera) records from Britain (excluding Northern Ireland and Channel Islands) up to August 2022 from the National Trichoptera (Caddisfly) Recording Scheme",
              "publishingOrganizationKey": "0c392aa0-a452-4254-be5c-e49dd60e9b02",
              "publishingOrganizationTitle": "Biological Records Centre"
            }
          },
          {
            "key": "686c1b9b-5f29-4e1f-8c28-f9779d264579",
            "count": 30486,
            "dataset": {
              "title": "Porcupine Marine Natural History Society Dataset",
              "publishingOrganizationKey": "f0a23325-1a1d-4b4c-a192-63765963d0a4",
              "publishingOrganizationTitle": "Porcupine Marine Natural History Society"
            }
          },
          {
            "key": "2e3454ce-5b2d-4bf4-bc23-ca5769f58137",
            "count": 15664,
            "dataset": {
              "title": "The Scottish Squirrel Database",
              "publishingOrganizationKey": "d98506d8-5ab1-4a26-9ef1-766bdb54304f",
              "publishingOrganizationTitle": "Scottish Wildlife Trust"
            }
          },
          {
            "key": "6f6b1102-5baa-4e24-86be-073a90b14db0",
            "count": 9146,
            "dataset": {
              "title": "1915-2016 Department for Environment Food & Rural Affairs (Defra), Marine Strategy Framework Directive (MSFD) Collation of invasive non-indigenous species",
              "publishingOrganizationKey": "f6b48504-1651-4a49-a88d-c2bc6178694d",
              "publishingOrganizationTitle": "Marine Biological Association"
            }
          },
          {
            "key": "4f272892-7a07-434f-8a69-7032826bcfb3",
            "count": 7271,
            "dataset": {
              "title": "Dipterists Forum: Field Week 2018 (Stoke)",
              "publishingOrganizationKey": "b663df19-4d5d-4139-96bb-32a83e24113f",
              "publishingOrganizationTitle": "Dipterists Forum"
            }
          },
          {
            "key": "340984fa-507b-4aa6-b59c-cce1dcee339f",
            "count": 7207,
            "dataset": {
              "title": "Records from the RHS insect reference collection",
              "publishingOrganizationKey": "f6213f74-d638-4907-a96d-26ca3b5da0c7",
              "publishingOrganizationTitle": "Royal Horticultural Society"
            }
          },
          {
            "key": "53f13c8f-413e-4537-bda6-98666cd7975f",
            "count": 7112,
            "dataset": {
              "title": "Other BSBI Scottish data up to 2016",
              "publishingOrganizationKey": "aa569acf-991d-4467-b327-8442f30ddbd2",
              "publishingOrganizationTitle": "Botanical Society of Britain & Ireland"
            }
          },
          {
            "key": "b52cb0c3-c024-46c4-b7b2-d635400ff6d1",
            "count": 6965,
            "dataset": {
              "title": "Echinoids_occurrences_Southern_Ocean",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "d6cd327a-7911-48e5-93e5-8664cb8a4ea8",
            "count": 6802,
            "dataset": {
              "title": "Dipterists Forum: Field Week 2017 (Snowdonia)",
              "publishingOrganizationKey": "b663df19-4d5d-4139-96bb-32a83e24113f",
              "publishingOrganizationTitle": "Dipterists Forum"
            }
          },
          {
            "key": "07a203b7-21a7-4c01-b8a4-cf906f4bc1c0",
            "count": 6517,
            "dataset": {
              "title": "1778-1998 Ivor Rees North Wales Marine Fauna Ad-hoc sightings shore and ship-based surveys",
              "publishingOrganizationKey": "f6b48504-1651-4a49-a88d-c2bc6178694d",
              "publishingOrganizationTitle": "Marine Biological Association"
            }
          },
          {
            "key": "cf8107e1-68be-4c76-a71d-05d96aeea4cb",
            "count": 6413,
            "dataset": {
              "title": "Dipterists Forum: Field Week 2016 (Canterbury)",
              "publishingOrganizationKey": "b663df19-4d5d-4139-96bb-32a83e24113f",
              "publishingOrganizationTitle": "Dipterists Forum"
            }
          },
          {
            "key": "e0074b38-e321-4ea9-844f-73a14a753283",
            "count": 4707,
            "dataset": {
              "title": "British bird eggs in the collections of World Museum, National Museums Liverpool",
              "publishingOrganizationKey": "31f13427-163d-4422-a28f-6f5d14ae2017",
              "publishingOrganizationTitle": "World Museum, National Museums Liverpool"
            }
          },
          {
            "key": "eaf6dd00-91ae-4c7a-9966-b4b582404ef6",
            "count": 4596,
            "dataset": {
              "title": "British bird study skins in the collections of World Museum, National Museums Liverpool",
              "publishingOrganizationKey": "31f13427-163d-4422-a28f-6f5d14ae2017",
              "publishingOrganizationTitle": "World Museum, National Museums Liverpool"
            }
          },
          {
            "key": "34f8683a-dfc0-46b8-acf6-390fe5ca6b92",
            "count": 4372,
            "dataset": {
              "title": "Heliconiine Butterfly Collection Records from University of Cambridge",
              "publishingOrganizationKey": "a8a63f81-fdbf-40e3-8a99-0d3832de262b",
              "publishingOrganizationTitle": "Department of Zoology, Cambridge"
            }
          },
          {
            "key": "36555a0c-8361-42c4-9f78-805816266f2e",
            "count": 3874,
            "dataset": {
              "title": "BSBI data from several English counties, up to 2015",
              "publishingOrganizationKey": "aa569acf-991d-4467-b327-8442f30ddbd2",
              "publishingOrganizationTitle": "Botanical Society of Britain & Ireland"
            }
          },
          {
            "key": "0ff1dbf3-7e14-41ec-9394-3c5813fee491",
            "count": 3328,
            "dataset": {
              "title": "Sciomyzidae Recording Scheme",
              "publishingOrganizationKey": "b663df19-4d5d-4139-96bb-32a83e24113f",
              "publishingOrganizationTitle": "Dipterists Forum"
            }
          },
          {
            "key": "1948a896-92c8-42de-a01a-38176a407e5a",
            "count": 2591,
            "dataset": {
              "title": "1848-1982 Lundy Field Society The Marine Fauna of Lundy",
              "publishingOrganizationKey": "f6b48504-1651-4a49-a88d-c2bc6178694d",
              "publishingOrganizationTitle": "Marine Biological Association"
            }
          },
          {
            "key": "ff3984d7-84bd-4f3a-b843-666faa4c1696",
            "count": 2121,
            "dataset": {
              "title": "Stable isotope ratios of C, N and S in Southern Ocean sea stars (1985-2017)",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "850058b9-c4a8-4c9c-bc19-d3354117024c",
            "count": 1970,
            "dataset": {
              "title": "Dipterists Forum: Field Week 1981 (Kent)",
              "publishingOrganizationKey": "b663df19-4d5d-4139-96bb-32a83e24113f",
              "publishingOrganizationTitle": "Dipterists Forum"
            }
          },
          {
            "key": "be31fcc4-19ae-4f80-b496-20f2119d4062",
            "count": 1968,
            "dataset": {
              "title": "Echinoids_Kerguelen_Plateau_1872_2015",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "5850a253-4e7c-44ec-a784-87a52fd0556a",
            "count": 1733,
            "dataset": {
              "title": "Conchological Society of Great Britain & Ireland: non-marine molluscs (fossil & subfossil records)",
              "publishingOrganizationKey": "dccfcdcf-d272-45c8-85cb-e3dbf18b8a34",
              "publishingOrganizationTitle": "Conchological Society of Great Britain & Ireland"
            }
          },
          {
            "key": "dac0a667-6beb-4c18-a456-e2a5bb43757d",
            "count": 1491,
            "dataset": {
              "title": "Bird study skins held by Leeds Museums and Galleries (non-UK records)",
              "publishingOrganizationKey": "afdb4b0a-2b16-4abc-99d3-03ba8289aeac",
              "publishingOrganizationTitle": "Leeds Museums and Galleries"
            }
          },
          {
            "key": "1e7b6980-0842-4c4a-8b14-541b95d2ed3c",
            "count": 1330,
            "dataset": {
              "title": "Sea spiders (Arthropoda, Pycnogonida) from ten recent research expeditions to the Antarctic Peninsula, Scotia Arc and Weddell Sea - data",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "8ef95309-811f-4c3b-a329-a85368e774c9",
            "count": 1168,
            "dataset": {
              "title": "Scottish SNH-funded BSBI records",
              "publishingOrganizationKey": "aa569acf-991d-4467-b327-8442f30ddbd2",
              "publishingOrganizationTitle": "Botanical Society of Britain & Ireland"
            }
          },
          {
            "key": "d03ce806-e16f-4cdb-a964-0b965523b908",
            "count": 983,
            "dataset": {
              "title": "DNA barcoding the fishes of Lizard Island (Great Barrier Reef)",
              "publishingOrganizationKey": "92f51af1-e917-49bc-a8ed-014ed3a77bec",
              "publishingOrganizationTitle": "Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow"
            }
          },
          {
            "key": "7bfd05a1-2e21-48d4-b49f-e338ad524ecf",
            "count": 960,
            "dataset": {
              "title": "An annotated checklist of the Araceae, Leguminosae and Myrtaceae of the department of Boyacá, Colombia",
              "publishingOrganizationKey": "061b4f20-f241-11da-a328-b8a03c50a862",
              "publishingOrganizationTitle": "Royal Botanic Gardens, Kew"
            }
          },
          {
            "key": "4f174243-a6e2-4ab3-99cb-129d2a6267e7",
            "count": 709,
            "dataset": {
              "title": "Water Beetle Surveys from Britain and Ireland",
              "publishingOrganizationKey": "76e846b0-1332-411e-a4fc-4e2251bfeea5",
              "publishingOrganizationTitle": "Balfour-Browne Club"
            }
          },
          {
            "key": "57fa062c-ac30-4f3f-a8ec-9d210e913415",
            "count": 638,
            "dataset": {
              "title": "MNA (Section of Genoa) - Marine Biological Samples",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "efb5e82d-477a-4a2e-a944-712963559db4",
            "count": 555,
            "dataset": {
              "title": "British bird study skins held by Leeds Museums and Galleries",
              "publishingOrganizationKey": "afdb4b0a-2b16-4abc-99d3-03ba8289aeac",
              "publishingOrganizationTitle": "Leeds Museums and Galleries"
            }
          },
          {
            "key": "4d30e8fd-de38-48d4-a977-25a43d607ed8",
            "count": 454,
            "dataset": {
              "title": "British Reptiles & Amphibians in the collections of World Museum Liverpool",
              "publishingOrganizationKey": "31f13427-163d-4422-a28f-6f5d14ae2017",
              "publishingOrganizationTitle": "World Museum, National Museums Liverpool"
            }
          },
          {
            "key": "7b506316-f762-11e1-a439-00145eb45e9a",
            "count": 440,
            "dataset": {
              "title": "Antarctic and Subantarctic Asteroid zoogeography",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "23cdb7f0-a1e4-4821-9986-10e92c5378e4",
            "count": 439,
            "dataset": {
              "title": "Sumner, D.P. 2020, European Micropezids & Tanypezids, Published Papers Part A Occurrence Dataset",
              "publishingOrganizationKey": "1d7ce54a-cdac-46a3-8279-f41a4a936776",
              "publishingOrganizationTitle": "European Micropezids & Tanypezids"
            }
          },
          {
            "key": "313bdea4-4517-4695-aee4-78286689c3b4",
            "count": 372,
            "dataset": {
              "title": "1966-1986 T.G. Skinner Solway Firth Occurrence of some prominent zooplankton",
              "publishingOrganizationKey": "f6b48504-1651-4a49-a88d-c2bc6178694d",
              "publishingOrganizationTitle": "Marine Biological Association"
            }
          },
          {
            "key": "28120c52-2b34-4db4-b348-812ee1eaf958",
            "count": 363,
            "dataset": {
              "title": "Stable isotope ratios and elemental contents of C, N and S in benthic organisms sampled during the PROTEKER 5 summer campaign in Kerguelen Islands (2016) - data",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "7b554a7a-f762-11e1-a439-00145eb45e9a",
            "count": 362,
            "dataset": {
              "title": "Museo Argentino de Ciencias Naturales (MACN), Buenos Aires: sea stars collection (Asteroidea, Echinodermata)",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "fcc25f03-8437-4ea3-859e-67866de5cb80",
            "count": 347,
            "dataset": {
              "title": "Sea cucumbers (Echinodemata, Holothuroidea) from the JR275 expedition to the Eastern Weddell Sea, Antarctica - Data",
              "publishingOrganizationKey": "104e9c96-791b-4f14-978c-f581cb214912",
              "publishingOrganizationTitle": "SCAR - AntOBIS"
            }
          },
          {
            "key": "25bf34e6-48ef-41aa-9b62-876ca0c66a2a",
            "count": 345,
            "dataset": {
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MortenHofft commented 2 years ago

So result nr 2 Natural History Museum (London) Collection Specimens has 4949975 specimens that could not be matched to GrSciColl. E.g. https://www.gbif.org/occurrence/1825885751 is matched to an institution but not to a collection

lmfrench commented 1 year ago

Thank you, we will take a look through, and start to contact these institutions. Some of these institutions do have a correct fuzzy match with GrSCiColl e.g. we know that NHM does appear on the UK portal (although we are looking at updating the NHM info, using the information you provided in #1)

TaraWainwright commented 1 year ago

Institutions not on GRSciColl have been contacted