A biodiversity dataset graph: https://jhpoelen.nl/bees. 2020. hash://sha256/85138e506a29fb73099fb050372d8a379794ab57fe4bfdf141743db0de2b985c
Created using Preston v0.2.0 on 2020-09-12T05:54:48.034Z.
Are you looking for a way to have fast, local access to 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?
Would you like to help preserve some (or all) of iDigBio’s images and their associated specimen data?
This automatically generated website contains a versioned archive of a custom selection of specimen records and associated media. The selection is made using the iDigBio Search API, a powerful search engine powered by Elastic Search that contains over 130M vouchered specimen records. The 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://search.idigbio.org/v2/search/records/?rq=%7B%22family%22%3A%22Andrenidae%22%2c%22hasImage%22%3A%22true%22%7D&limit=10&offset=0"
# 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 "https://jhpoelen.nl/bees/data"
Also, you can query the idigbio records available through this site via the api at https://jhpoelen.nl/bees/data.json. With this, you can programmatically access the data and select the records you are interested in. For instance, you can show the first record by executing:
$ curl "https://jhpoelen.nl/bees/data.json" | jq -c 'select(.type == "records")' | head -n1
[{"uuid":"16f6de61-541c-46b1-b7e7-d8303e6f53db","type":"records","etag":"6e173548e1abf63237c9d14c633cc95298633332","data":{"dwc:identificationRemarks":"Labels: Bodega Calif Apl 3; type 17219; Spinoliella puellae Ckll cotype.","dwc:specificEpithet":"puellae","dwc:countryCode":"US","dwc:county":"Sonoma","dwc:recordedBy":"[no agent data]","dwc:georeferenceSources":"GEOLocate","dwc:order":"Hymenoptera","dcterms:references":"http://mczbase.mcz.harvard.edu/guid/MCZ:Ent:17219","dwc:individualCount":"1","dwc:occurrenceID":"MCZ:Ent:17219","dwc:dateIdentified":"2012","dcterms:language":"en","id":"MCZ:Ent:17219","dwc:stateProvince":"California","dwc:institutionCode":"MCZ","dwc:country":"United States","dwc:typeStatus":"Syntype of Spinoliella puellae","dwc:collectionCode":"Ent","dcterms:rightsHolder":"President and Fellows of Harvard College","dwc:kingdom":"Animalia","dwc:decimalLatitude":"38.345194","dwc:georeferenceVerificationStatus":"verified by MCZ collection","dwc:basisOfRecord":"PreservedSpecimen","dwc:genus":"Nomadopsis","dwc:continent":"North America","dwc:preparations":"whole animal (mounted)","dwc:identifiedBy":"Cockerell","dwc:dynamicProperties":"{}","dwc:disposition":"not applicable","dwc:ownerInstitutionCode":"Museum of Comparative Zoology, Harvard University","dwc:higherClassification":"Animalia Arthropoda Hexapoda Insecta Pterygota Hymenoptera Andrenidae Nomadopsis puellae","dwc:phylum":"Arthropoda","dwc:locality":"Bodega","dwc:institutionID":"b4640710-8e03-11d8-b956-b8a03c50a862","dwc:geodeticDatum":"WGS84","dwc:class":"Insecta","dwc:catalogNumber":"17219","dwc:nomenclaturalCode":"ICZN","dcterms:type":"PhysicalObject","dwc:Identification":[{"dwc:identifiedBy":"Cockerell","dwc:identificationRemarks":"; Determination year is a proxy for unknown data. It will be updated when year is known Determinations made by Cockerell","dwc:identificationVerificationStatus":"expert ID","coreid":"MCZ:Ent:17219","dwc:identificationID":"3152831","dwc:dateIdentified":"2012","dwc:scientificName":"Nomadopsis puellae"},{"coreid":"MCZ:Ent:17219","dwc:identifiedBy":"Theodore D. A. Cockerell","dwc:scientificName":"Spinoliella puellae","dwc:identificationVerificationStatus":"type ID","dwc:identificationID":"3630139"},{"dwc:identifiedBy":"Cockerell","dwc:identificationVerificationStatus":"Type Publication","dwc:scientificNameAuthorship":"Cockerell","dwc:identificationReferences":"Cockerell, T. D. A.. 1933. Bees collected at Borego, California, by Wilmatte P. Cockerell & Milene Porter. Pan-Pacific Entomologist 9:25-28","dwc:typeStatus":"Syntype","coreid":"MCZ:Ent:17219","dwc:identificationID":"588174315305405521Syntype","dwc:phylum":"Arthropoda","dwc:dateIdentified":"1933","dwc:scientificName":"Spinoliella puellae"}],"dwc:higherGeography":"North America: United States: California: Sonoma","dwc:decimalLongitude":"-122.973888","dwc:coordinateUncertaintyInMeters":"1968","dwc:otherCatalogNumbers":"type number=17219","dwc:verbatimLocality":"Bodega Calif Apl 3;","dwc:georeferencedBy":"Jeremy Kisala","dwc:verbatimEventDate":"Apl 3","dwc:family":"Andrenidae","dwc:verbatimCoordinateSystem":"decimal degrees","dwc:georeferenceProtocol":"GEOLocate","dcterms:modified":"2020-01-31 12:49:09.0","dwc:scientificName":"Nomadopsis puellae"},"indexTerms":{"individualcount":1,"geopoint":{"lat":38.345194,"lon":-122.97388800000002},"family":"andrenidae","recordset":"271a9ce9-c6d3-4b63-a722-cb0adc48863f","dqs":0.391304347826087,"stateprovince":"california","county":"sonoma","phylum":"arthropoda","catalognumber":"17219","specificepithet":"puellae","continent":"north america","datemodified":"2020-07-24T20:04:57.585704+00:00","uuid":"16f6de61-541c-46b1-b7e7-d8303e6f53db","countrycode":"usa","basisofrecord":"preservedspecimen","collector":"[no agent data]","institutioncode":"mcz","mediarecords":["6e0122c9-28b7-4bd2-9a0c-46bb3346c713","0b5b4499-1055-4adc-9017-be1dc5914c13","0c262b4e-3d2e-4a91-8968-45615e9ba6a5","6e0df331-3ccf-4b7c-8e8d-7bc512d69a1a","2337cdf9-3cc8-431b-ba45-5cb52271d320"],"verbatimlocality":"bodega calif apl 3;","etag":"6e173548e1abf63237c9d14c633cc95298633332","typestatus":"syntype of spinoliella puellae","hasMedia":true,"hasImage":true,"kingdom":"animalia","highertaxon":"animalia arthropoda hexapoda insecta pterygota hymenoptera andrenidae nomadopsis puellae","scientificname":"nomadopsis puellae","indexData":{"dwc:identificationRemarks":"Labels: Bodega Calif Apl 3; type 17219; Spinoliella puellae Ckll cotype.","dwc:specificEpithet":"puellae","dwc:countryCode":"US","dwc:county":"Sonoma","dwc:recordedBy":"[no agent data]","idigbio:uuid":"16f6de61-541c-46b1-b7e7-d8303e6f53db","dwc:locality":"Bodega","dwc:order":"Hymenoptera","dcterms:references":"http://mczbase.mcz.harvard.edu/guid/MCZ:Ent:17219","dwc:individualCount":"1","idigbio:recordIds":["271a9ce9-c6d3-4b63-a722-cb0adc48863f\\mcz:ent:17219"],"dwc:occurrenceID":"MCZ:Ent:17219","dwc:dateIdentified":"2012","idigbio:etag":"6e173548e1abf63237c9d14c633cc95298633332","dcterms:language":"en","dcterms:rightsHolder":"President and Fellows of Harvard College","idigbio:parent":"271a9ce9-c6d3-4b63-a722-cb0adc48863f","dwc:stateProvince":"California","dwc:country":"United States","dwc:typeStatus":"Syntype of Spinoliella puellae","dwc:collectionCode":"Ent","id":"MCZ:Ent:17219","dwc:kingdom":"Animalia","dwc:decimalLatitude":"38.345194","dwc:georeferenceVerificationStatus":"verified by MCZ collection","dwc:basisOfRecord":"PreservedSpecimen","dwc:genus":"Nomadopsis","dwc:continent":"North America","dwc:preparations":"whole animal (mounted)","idigbio:isocountrycode":"usa","dwc:identifiedBy":"Cockerell","dwc:dynamicProperties":"{}","dwc:class":"Insecta","dwc:disposition":"not applicable","dwc:geodeticDatum":"WGS84","idigbio:siblings":{"mediarecord":["6e0122c9-28b7-4bd2-9a0c-46bb3346c713","0b5b4499-1055-4adc-9017-be1dc5914c13","0c262b4e-3d2e-4a91-8968-45615e9ba6a5","6e0df331-3ccf-4b7c-8e8d-7bc512d69a1a","2337cdf9-3cc8-431b-ba45-5cb52271d320"]},"dwc:ownerInstitutionCode":"Museum of Comparative Zoology, Harvard University","flag_idigbio_isocountrycode_added":true,"dwc:phylum":"Arthropoda","idigbio:dateModified":"2020-07-24T20:04:57.585704","dwc:georeferenceSources":"GEOLocate","dwc:institutionID":"b4640710-8e03-11d8-b956-b8a03c50a862","dwc:institutionCode":"MCZ","dwc:higherClassification":"Animalia Arthropoda Hexapoda Insecta Pterygota Hymenoptera Andrenidae Nomadopsis puellae","dwc:catalogNumber":"17219","dwc:nomenclaturalCode":"ICZN","dcterms:type":"PhysicalObject","dwc:Identification":[{"dwc:identifiedBy":"Cockerell","dwc:identificationRemarks":"; Determination year is a proxy for unknown data. It will be updated when year is known Determinations made by Cockerell","dwc:identificationVerificationStatus":"expert ID","coreid":"MCZ:Ent:17219","dwc:identificationID":"3152831","dwc:dateIdentified":"2012","dwc:scientificName":"Nomadopsis puellae"},{"coreid":"MCZ:Ent:17219","dwc:identifiedBy":"Theodore D. A. Cockerell","dwc:scientificName":"Spinoliella puellae","dwc:identificationID":"3630139","dwc:identificationVerificationStatus":"type ID"},{"dwc:identifiedBy":"Cockerell","dwc:identificationVerificationStatus":"Type Publication","dwc:identificationID":"588174315305405521Syntype","dwc:identificationReferences":"Cockerell, T. D. A.. 1933. Bees collected at Borego, California, by Wilmatte P. Cockerell & Milene Porter. Pan-Pacific Entomologist 9:25-28","dwc:typeStatus":"Syntype","coreid":"MCZ:Ent:17219","dwc:scientificNameAuthorship":"Cockerell","dwc:phylum":"Arthropoda","dwc:dateIdentified":"1933","dwc:scientificName":"Spinoliella puellae"}],"dwc:higherGeography":"North America: United States: California: Sonoma","dwc:decimalLongitude":"-122.973888","dwc:scientificName":"Nomadopsis puellae","dwc:otherCatalogNumbers":"type number=17219","dwc:verbatimLocality":"Bodega Calif Apl 3;","dwc:georeferencedBy":"Jeremy Kisala","dwc:verbatimEventDate":"Apl 3","dwc:family":"Andrenidae","dwc:verbatimCoordinateSystem":"decimal degrees","flag_taxon_match_failed":true,"dwc:georeferenceProtocol":"GEOLocate","dcterms:modified":"2020-01-31 12:49:09.0","dwc:coordinateUncertaintyInMeters":"1968"},"coordinateuncertainty":1968,"class":"insecta","occurrenceid":"mcz:ent:17219","institutionid":"b4640710-8e03-11d8-b956-b8a03c50a862","country":"united states","locality":"bodega","collectioncode":"ent","flags":["idigbio_isocountrycode_added","taxon_match_failed"],"verbatimeventdate":"apl 3","recordids":["271a9ce9-c6d3-4b63-a722-cb0adc48863f\\mcz:ent:17219"],"genus":"nomadopsis","order":"hymenoptera"}}]
Or, use jq to select the records with scientific name matching Liphanthus sabulosus:
curl -s "https://jhpoelen.nl/bees/data.json" | jq -c 'select(.data["dwc:scientificName"] == "Liphanthus sabulosus")'
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 the iDigBio search API
preston update "https://search.idigbio.org/v2/search/records/?rq=%7B%22family%22%3A%22Andrenidae%22%2c%22hasImage%22%3A%22true%22%7D&limit=10&offset=0"
# update Jekyll site with archived content
preston copyTo --type jekyll .
This archived dataset includes 10 specimen records and 39 media records.
The first 10 records and their associated media included in this data archive are:
