A biodiversity dataset graph: http://jhpoelen.nl/fieldmuseum-lice. 2021. hash://sha256/8478d61dedc0a582566934724382c5fa79c2ca5756d6d39c47ea4ad2e7d07e69
Created using Preston v0.2.5 and Jekyll v3.9.0 on 2021-02-26T19:14:43.666Z.
Are you looking for a way to have fast, local access to GBIF/iDigBio indexed records and media?
Would you like to have an exact copy of the images in your research dataset?
Do you want to include latest research data while keeping your original data around?
This automatically generated website contains a versioned archive of a custom selection of occurrence/specimen records and associated media. The selection is made using currently available biodiversity search indexes like the iDigBio Search API or the GBIF Occurrence Search API. The indexed data is archived using Preston, a biodiversity data tracker that can version entire biodiversity dataset networks. Finally, the website is generated from the archived content using Jekyll, the static site generator that powers GitHub pages.
This biodiversity data archive website was created with the following steps:
# first, create a new blank jekyll site (tested on Jekyll v4.0.1)
jekyll new [site_dir] --blank
cd [site_dir]
# archive 10 iDigBio indexed Andrenidae records and related images
preston track "https://api.gbif.org/v1/occurrence/search?dataset_key=7931dcab-94f1-46ce-8092-56e4335423de&taxon_key=8557082&taxon_key=1032837"
# generate Jekyll site for archived content
preston copyTo --type jekyll .
# launch website and visit http://localhost:4000 in your browser
jekyll s
You can clone an exact copy of the entire biodiversity data archive using:
preston clone "http://jhpoelen.nl/fieldmuseum-lice/data"
Also, you can query the indexed data available through this site via the api at http://jhpoelen.nl/fieldmuseum-lice/data.json.
With this, you can programmatically access the data and select the records you are interested in.
For instance, using curl and jq, you can show the first record by executing:
$ curl "http://jhpoelen.nl/fieldmuseum-lice/data.json" | jq -c 'select(.type == "records")' | head -n1
[]
Or, look for an occurrence with images indexed by GBIF:
$ curl "http://jhpoelen.nl/fieldmuseum-lice/data.json" | jq -c 'select(.media[].type == "StillImage")' | head -n1
[{"key":1142282026,"datasetKey":"7931dcab-94f1-46ce-8092-56e4335423de","publishingOrgKey":"7b8aff00-a9f8-11d8-944b-b8a03c50a862","installationKey":"3b84ff5b-79ce-427c-acb7-b4004e160f66","publishingCountry":"US","protocol":"DWC_ARCHIVE","lastCrawled":"2020-12-11T16:42:57.147+00:00","lastParsed":"2020-12-15T23:38:09.310+00:00","crawlId":204,"hostingOrganizationKey":"7b8aff00-a9f8-11d8-944b-b8a03c50a862","extensions":{"http://rs.tdwg.org/ac/terms/Multimedia":[{"http://purl.org/dc/terms/identifier":"dae1314f-0793-4c01-bef0-ccbf8fe52d36","http://ns.adobe.com/xap/1.0/rights/Owner":"Field Museum of Natural History","http://purl.org/dc/elements/1.1/format":"jpeg","http://purl.org/dc/elements/1.1/type":"Image","http://rs.tdwg.org/ac/terms/providerManagedID":"681579","http://ns.adobe.com/exif/1.0/PixelYDimension":"2022","http://rs.tdwg.org/ac/terms/metadataLanguageLiteral":"eng","http://ns.adobe.com/photoshop/1.0/Credit":"Please cite this as: (c) The Field Museum (DATE) CC-BY-NC","http://rs.tdwg.org/ac/terms/IDofContainingCollection":"http://biocol.org/urn:lsid:biocol.org:col:34795","http://purl.org/dc/elements/1.1/creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","http://ns.adobe.com/xap/1.0/CreateDate":"2014","http://purl.org/dc/terms/description":"28520 Menacanthus werneri PT d IN","http://rs.tdwg.org/ac/terms/hashValue":"004568464f0a986701419a67e998e57e","http://ns.adobe.com/exif/1.0/PixelXDimension":"1334","http://purl.org/dc/terms/title":"28520 Menacanthus werneri PT d IN","http://rs.tdwg.org/ac/terms/accessURI":"https://fm-digital-assets.fieldmuseum.org/681/579/28520_Menacanthus_werneri_PT_d_IN.jpg","http://purl.org/dc/elements/1.1/rights":"[Copyright] Field Museum of Natural History - CC BY-NC","http://ns.adobe.com/xap/1.0/rights/WebStatement":"https://www.fieldmuseum.org/field-museum-natural-history-conditions-and-suggested-norms-use-collections","http://rs.tdwg.org/ac/terms/hasServiceAccessPoint":"https://mm.fieldmuseum.org/dae1314f-0793-4c01-bef0-ccbf8fe52d36","http://rs.tdwg.org/ac/terms/tag":"Phthiraptera slide | Menacanthus","http://rs.tdwg.org/ac/terms/hashFunction":"MD5","http://ns.adobe.com/xap/1.0/MetadataDate":"2020-08-21","http://rs.tdwg.org/ac/terms/variantLiteral":"mediumQualityFurtherInformationURL"},{"http://purl.org/dc/terms/identifier":"e433521e-ce22-49c1-a141-9ef6858c9ee6","http://ns.adobe.com/xap/1.0/rights/Owner":"Field Museum of Natural History","http://purl.org/dc/elements/1.1/format":"jpeg","http://purl.org/dc/elements/1.1/type":"Image","http://rs.tdwg.org/ac/terms/providerManagedID":"681582","http://ns.adobe.com/exif/1.0/PixelYDimension":"1945","http://rs.tdwg.org/ac/terms/metadataLanguageLiteral":"eng","http://ns.adobe.com/photoshop/1.0/Credit":"Please cite this as: (c) The Field Museum (DATE) CC-BY-NC","http://rs.tdwg.org/ac/terms/IDofContainingCollection":"http://biocol.org/urn:lsid:biocol.org:col:34795","http://purl.org/dc/elements/1.1/creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","http://ns.adobe.com/xap/1.0/CreateDate":"2014","http://purl.org/dc/terms/description":"28520 Menacanthus werneri PT v IN","http://rs.tdwg.org/ac/terms/hashValue":"9ead4d764ff760841cc5e51f43d850d4","http://ns.adobe.com/exif/1.0/PixelXDimension":"1334","http://purl.org/dc/terms/title":"28520 Menacanthus werneri PT v IN","http://rs.tdwg.org/ac/terms/accessURI":"https://fm-digital-assets.fieldmuseum.org/681/582/28520_Menacanthus_werneri_PT_v_IN.jpg","http://purl.org/dc/elements/1.1/rights":"[Copyright] Field Museum of Natural History - CC BY-NC","http://ns.adobe.com/xap/1.0/rights/WebStatement":"https://www.fieldmuseum.org/field-museum-natural-history-conditions-and-suggested-norms-use-collections","http://rs.tdwg.org/ac/terms/hasServiceAccessPoint":"https://mm.fieldmuseum.org/e433521e-ce22-49c1-a141-9ef6858c9ee6","http://rs.tdwg.org/ac/terms/tag":"Phthiraptera slide | Menacanthus","http://rs.tdwg.org/ac/terms/hashFunction":"MD5","http://ns.adobe.com/xap/1.0/MetadataDate":"2020-08-21","http://rs.tdwg.org/ac/terms/variantLiteral":"mediumQualityFurtherInformationURL"},{"http://purl.org/dc/terms/identifier":"e4d5214e-1061-4146-9d12-4c19542fd026","http://ns.adobe.com/xap/1.0/rights/Owner":"Field Museum of Natural History","http://purl.org/dc/elements/1.1/format":"jpeg","http://purl.org/dc/elements/1.1/type":"Image","http://rs.tdwg.org/ac/terms/providerManagedID":"564155","http://ns.adobe.com/exif/1.0/PixelYDimension":"4000","http://rs.tdwg.org/ac/terms/metadataLanguageLiteral":"eng","http://ns.adobe.com/photoshop/1.0/Credit":"Please cite this as: (c) The Field Museum (DATE) CC-BY-NC","http://rs.tdwg.org/ac/terms/IDofContainingCollection":"http://biocol.org/urn:lsid:biocol.org:col:34795","http://purl.org/dc/elements/1.1/creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","http://ns.adobe.com/xap/1.0/CreateDate":"2014","http://purl.org/dc/terms/description":"28520 Menacanthus werneri PT slide IN","http://rs.tdwg.org/ac/terms/hashValue":"633d0ccc6951a8e669f766d3005ca592","http://ns.adobe.com/exif/1.0/PixelXDimension":"2248","http://purl.org/dc/terms/title":"28520 Menacanthus werneri PT slide IN","http://rs.tdwg.org/ac/terms/accessURI":"https://fm-digital-assets.fieldmuseum.org/564/155/28520_Menacanthus_werneri_PT_slide_IN.JPG","http://purl.org/dc/elements/1.1/rights":"[Copyright] Field Museum of Natural History - CC BY-NC","http://ns.adobe.com/xap/1.0/rights/WebStatement":"https://www.fieldmuseum.org/field-museum-natural-history-conditions-and-suggested-norms-use-collections","http://rs.tdwg.org/ac/terms/hasServiceAccessPoint":"https://mm.fieldmuseum.org/e4d5214e-1061-4146-9d12-4c19542fd026","http://rs.tdwg.org/ac/terms/tag":"Phthiraptera slide | Menacanthus | Paratype","http://rs.tdwg.org/ac/terms/hashFunction":"MD5","http://ns.adobe.com/xap/1.0/MetadataDate":"2020-08-21","http://rs.tdwg.org/ac/terms/variantLiteral":"mediumQualityFurtherInformationURL"}]},"basisOfRecord":"PRESERVED_SPECIMEN","individualCount":1,"occurrenceStatus":"PRESENT","sex":"MALE","lifeStage":"Adult","taxonKey":6935007,"kingdomKey":1,"phylumKey":54,"classKey":216,"orderKey":7612838,"familyKey":2783,"genusKey":1032837,"speciesKey":6935007,"acceptedTaxonKey":6935007,"scientificName":"Menacanthus werneri Emerson & R.A.Ward, 1958","acceptedScientificName":"Menacanthus werneri Emerson & R.A.Ward, 1958","kingdom":"Animalia","phylum":"Arthropoda","order":"Psocodea","family":"Menoponidae","genus":"Menacanthus","species":"Menacanthus werneri","genericName":"Menacanthus","specificEpithet":"werneri","taxonRank":"SPECIES","taxonomicStatus":"ACCEPTED","continent":"ASIA","stateProvince":"Palawan","year":1947,"month":3,"day":8,"eventDate":"1947-03-08T00:00:00","typeStatus":"PARATYPE","issues":["OCCURRENCE_STATUS_INFERRED_FROM_INDIVIDUAL_COUNT","INSTITUTION_MATCH_FUZZY","INSTITUTION_COLLECTION_MISMATCH"],"lastInterpreted":"2020-12-15T23:38:09.310+00:00","license":"http://creativecommons.org/publicdomain/zero/1.0/legalcode","identifiers":[],"media":[{"type":"StillImage","format":"jpeg","title":"28520 Menacanthus werneri PT slide IN","description":"28520 Menacanthus werneri PT slide IN","created":"2014-01-01T00:00:00.000+00:00","creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","license":"[Copyright] Field Museum of Natural History - CC BY-NC","rightsHolder":"Field Museum of Natural History","identifier":"https://fm-digital-assets.fieldmuseum.org/564/155/28520_Menacanthus_werneri_PT_slide_IN.JPG"},{"type":"StillImage","format":"image/jpeg","identifier":"http://fm-digital-assets.fieldmuseum.org/681/582/28520_Menacanthus_werneri_PT_v_IN.jpg"},{"references":"http://fm-digital-assets.fieldmuseum.org/564/155/28520_Menacanthus_werneri_PT_sli"},{"type":"StillImage","format":"image/jpeg","identifier":"http://fm-digital-assets.fieldmuseum.org/681/579/28520_Menacanthus_werneri_PT_d_IN.jpg"},{"type":"StillImage","format":"jpeg","title":"28520 Menacanthus werneri PT d IN","description":"28520 Menacanthus werneri PT d IN","created":"2014-01-01T00:00:00.000+00:00","creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","license":"[Copyright] Field Museum of Natural History - CC BY-NC","rightsHolder":"Field Museum of Natural History","identifier":"https://fm-digital-assets.fieldmuseum.org/681/579/28520_Menacanthus_werneri_PT_d_IN.jpg"},{"type":"StillImage","format":"jpeg","title":"28520 Menacanthus werneri PT v IN","description":"28520 Menacanthus werneri PT v IN","created":"2014-01-01T00:00:00.000+00:00","creator":"Field Museum of Natural History - Insects Division | GDI 2013-2015","license":"[Copyright] Field Museum of Natural History - CC BY-NC","rightsHolder":"Field Museum of Natural History","identifier":"https://fm-digital-assets.fieldmuseum.org/681/582/28520_Menacanthus_werneri_PT_v_IN.jpg"}],"facts":[],"relations":[],"gadm":{},"institutionKey":"e71f36f1-e271-4720-a604-3c5a1418e7aa","isInCluster":false,"class":"Insecta","countryCode":"PH","recordedByIDs":[],"identifiedByIDs":[],"country":"Philippines","rightsHolder":"The Field Mueum of Natural History","identifier":"327ec6a1-0674-498d-9d77-b87f195324ba","institutionID":"FMNH","higherGeography":"Philippines, Palawan, Philippines, Palawan: Iwahig Penal Colony","islandGroup":"Philippines","island":"Palawan","endDayOfYear":"8","locality":"Iwahig Penal Colony","fieldNumber":"Lou-1947-1718","language":"en","gbifID":"1142282026","collectionCode":"Insects","occurrenceID":"327ec6a1-0674-498d-9d77-b87f195324ba","type":"PhysicalObject","catalogNumber":"FMNHINS 0000 028 520","recordedBy":"H. Hoogstraal","organismID":"2800539","institutionCode":"FMNH","startDayOfYear":"8","ownerInstitutionCode":"FMNH","datasetID":"insects-02-dec-2020","accessRights":"https://www.fieldmuseum.org/about/copyright-information","collectionID":"Insects","higherClassification":"Animalia Arthropoda Insecta Phthiraptera Menoponidae"}]
Or, select archived iDigBio index records with scientific name matching Liphanthus sabulosus:
curl -s "http://jhpoelen.nl/fieldmuseum-lice/data.json" | jq -c 'select(.data["dwc:scientificName"] == "Liphanthus sabulosus")'
This biodiversity archive contains local copies of remote content.You can access a list of all archived location via the content registry at http://jhpoelen.nl/fieldmuseum-lice/registry.json. Here’s a way to get the first one:
$ curl -s "http://jhpoelen.nl/fieldmuseum-lice/registry.json" | head -n1
{"url":"https://api.gbif.org/v1/occurrence/search?dataset_key=7931dcab-94f1-46ce-8092-56e4335423de&taxon_key=8557082&taxon_key=1032837","verb":"http://purl.org/pav/hasVersion","hash":"hash://sha256/ded2858459bc6b698ee9b8d873cccbba4d8608800ff993243ed47200de8b1563","graphname":"urn:uuid:bf7bb499-7302-411f-b214-d5214e6bcfc7"}
The backbone of this biodiversity data archive is their provenance log, or knowledge graph. This knowledge graph is stored in in rdf/nquad format and can loaded into triple store and queried using SPARQL.
Because the log is stored in a text file you can easily read it. For instance, the first 10 lines of the provenance graph (or knowledge graph) can be seen when running:
curl -s "http://jhpoelen.nl/fieldmuseum-lice/data/84/78/8478d61dedc0a582566934724382c5fa79c2ca5756d6d39c47ea4ad2e7d07e69" | head
For more information about how to fully take advantage of this biodiversity data graph, please review preston documentation for use cases, concepts and architecture.
Many natural history collections are actively digitizing their collections. These collections are actively indexed by iDigBio as the new data records and media become available. This website can be updated to incorporate newly added or updated data by:
cd [site_dir]
# archive records and related images with criteria specified in some biodiversity search API
preston update "https://api.gbif.org/v1/occurrence/search?dataset_key=7931dcab-94f1-46ce-8092-56e4335423de&taxon_key=8557082&taxon_key=1032837"
# update Jekyll site with archived content
preston copyTo --type jekyll .
This archived dataset includes 0 iDigBio indexed specimen records, 0 iDigBio indexed media records, 110 GBIF indexed occurrence records, and 129 GBIF indexed images.
The first 10-20 records and their associated media included in this data archive are:
