pid-specimen-genbank
Introduction
To see the APIs in action use the notebook: https://github.com/sharifX/pid-specimen-genbank/blob/master/specimen-pid-genbank.ipynb
A page to demonstrate various identifiers and linkages.
Natural history collections held in museums preserve and archive various types of biological and geological specimens that provide a physical record of the biodiversity in the natural world. Together, these specimens and associated data (such as publications and molecular sequence data) represent an unparalleled resource to study the world's biodiversity. However, the current ecosystem of specimens and collection management globally is highly fragmented with discipline-specific data and metadata standards and institutional repositories. A consistent and sustainable approach to linking these physical specimens with other identifiable entities is then crucial for findability, accessibility, interoperability, and reproducibility i.e., achieving data ‘FAIRness’.
Within the DiSSCo project, we are proposing the idea of Digital Specimens that act as representations of physical specimens. We are envisioning a ‘unified knowledge graph’ where Digital Specimens sit as nodes in an interconnected graph of connections between specimens, and connections from specimens to third-party sources of data/information related to those specimens.
Background information
- Persistent Identfiers (PID)
"A persistent identifier (PI or PID) is a long-lasting reference to a document, file, web page, or other object. The term "persistent identifier" is usually used in the context of digital objects that are accessible over the Internet"
"A digital object (DO) is a sequence of bits, or a set of sequences of bits, incorporating a work or portion of a work or other information in which a party has rights or interests, or in which there is value, each of the sequences being structured in a way that is interpretable by one or more computational facilities. Each DO has, as an essential element, an associated unique persistent identifier, known as digital object identifier (referred to informally as a handle)."
- Physical and Digital Specimen ID
This is a physical specimen id (often times maintained in the collection management system by the collection holding institute) : B100586893. The URL associated with this physical specimen: http://herbarium.bgbm.org/object/B100586893
This is a Digital Specimen ID (20.5000.1025/c4942d87a9f89d8929c1 which is a handle): http://hdl.handle.net/20.5000.1025/c4942d87a9f89d8929c1
And links to the physical specimen id
curl -s -X GET http://nsidr.org:8080/objects/20.5000.1025/c4942d87a9f89d8929c1?jsonPointer=/physicalSpecimenId|jq
" B 10 0586893"
Example Use cases
Which specimens have associated sequences in GenBank?
Physical specimen/catalog id:
RMNH 6001
RMNH D 38033
RMNH:MOL:256470
RMNH:MOL:47312
Search in the ENA database
String search "RMNH*". We only grab a few fields and the first 5 records in tsv format.
curl -X POST -H "Content-Type: application/x-www-form-urlencoded" -d "result=sequence_release&query=specimen_voucher%3D%22RMNH*%22&fields=specimen_voucher%2Caccession%2Cscientific_name%2Ctax_id&limit=5&format=tsv" "https://www.ebi.ac.uk/ena/portal/api/search"
Output in tsv format:
| | | |
|------------------------------------------------------------------------------------------------------------------------|-----------|-----------------------------------|--------|
| specimen_voucher | accession | scientific_name | tax_id |
| RMNH 6001 Type specimen, Nationaal Natuurhistorisch Museum, Leiden (formerly Rijksmuseum van der Natuurlijke Historie) | AF371257 | Cylindraspis vosmaeri | 180178 |
| RMNH D 38033 | AM076944 | Stylodactylus serratus | 342640 |
| RMNH D42542 (Naturalis Museum Leiden) | AM180692 | Palicus caronii | 364890 |
| JWS700;RMNH:MOL:256470 | AY382068 | Albinaria puella puella | 256890 |
| SK616;RMNH:MOL:47312 | AY382076 | Isabellaria isabellina isabellina | 127721 |
How can I verify that these records are indeed currently housed in the Naturalis Biodiversity Center formerly Rijksmuseum van der Natuurlijke Historie?
EMBL record details https://www.ebi.ac.uk/ena/browser/api/embl/AM076944.1?lineLimit=1000
OLD ENA browser https://www.ebi.ac.uk/ena/data/view/AM076944
RN [2]
RA Cleva R., Van Wormhoudt A.E.;
RT "On two rare and poorly known species, Stylodactylus discissipe Bate, 1888,
RT and S. serratus A Milne Edwards, 1881 (crustacea decapoda :
RT Styodactylydae)";
RL Unpublished.
XX
DR MD5; 3cc4a3ac26715ebcc7bcdb8d4352b881.
XX
FH Key Location/Qualifiers
FH
FT source 1..300
FT /organism="Stylodactylus serratus"
FT /organelle="mitochondrion"
FT /mol_type="genomic DNA"
FT /country="Atlantic Ocean:Caribbean Islands St Vincent"
FT /isolation_source="sea water, trawl at -800m"
FT /specimen_voucher="RMNH D 38033"
FT /db_xref="taxon:342640"
FT rRNA 1..>300
FT /gene="16S rRNA"
FT /product="16S ribosomal RNA"
After some manual investigation (via gbif record https://www.gbif.org/occurrence/2434390604) we find this:
https://bioportal.naturalis.nl/specimen/RMNH.CRUS.D.38033
Looks like the ENA record is missing the full physical specimen id. How can we do this in a more efficient way?
Digital Specimen
Only if we had a digital object connecting all these links:
curl -s -X GET http://145.136.243.81:8080/objects/test/7ae4c781214bda021013|jq
{
"id": "test/7ae4c781214bda021013",
"scientificName": "Stylodactylus serratus Milne-Edwards, 1881",
"physicalSpecimenId": "RMNH.CRUS.D.38033",
"stableIdentifier": "https://data.biodiversitydata.nl/naturalis/specimen/RMNH.CRUS.D.38033",
"accession": "https://identifiers.org/ena.embl:AM076944",
"tax_id": "https://identifiers.org/taxonomy:342640"
}
Can I track down all the specimens in this paper?
Tenorio, Manuel J. & Castelin, Magalie, 2016, Genus Profundiconus Kuroda, 1956 (Gastropoda, Conoidea): Morphological and molecular studies, with the description of five new species from the Solomon Islands and New Caledonia, European Journal of Taxonomy 173, pp. 1-45: 19-21
http://dx.doi.org/10.5852/ejt.2016.173
Plazi link: http://treatment.plazi.org/id/24768796-CD1F-FFC6-FDED-1609FD27FE12
RDF LINK http://treatment.plazi.org/id/24768796-CD1F-FFC6-FDED-1609FD27FE12.rdf
This uses darwin core terms
grep 'dwc:specimenCode>' 24768796-CD1F-FFC6-FDED-1609FD27FE12.rdf
<dwc:specimenCode>IM-2007-34878</dwc:specimenCode>
<dwc:specimenCode>IM-2007-30935</dwc:specimenCode>
<dwc:specimenCode>IM-2007-30338</dwc:specimenCode>
<dwc:specimenCode>IM-2007- 34880</dwc:specimenCode>
<dwc:specimenCode>IM-2007-34879</dwc:specimenCode>
grep 'dwc:httpUri' 24768796-CD1F-FFC6-FDED-1609FD27FE12.rdf
<dwc:httpUri>http://coldb.mnhn.fr/catalognumber/mnhn/im/2007-34878</dwc:httpUri>
<dwc:httpUri>http://coldb.mnhn.fr/catalognumber/mnhn/im/2007-30935</dwc:httpUri>
<dwc:httpUri>http://coldb.mnhn.fr/catalognumber/mnhn/im/2007-30338</dwc:httpUri>
<dwc:httpUri>http://coldb.mnhn.fr/catalognumber/mnhn/im/2007-34880</dwc:httpUri>
<dwc:httpUri>http://coldb.mnhn.fr/catalognumber/mnhn/im/2007-34879</dwc:httpUri>
Other identifications
grep 'dwc:accessionNumber' 24768796-CD1F-FFC6-FDED-1609FD27FE12.rdf
<dwc:accessionNumber>KJ550352</dwc:accessionNumber>
Reading the pdf we also find several BOLD process ids which takes us to the barcode number (BIN)
http://www.boldsystems.org/index.php/Public_RecordView?processid=CONO296-08
processid sampleid recordID catalognum fieldnum institution_storing collection_code bin_uri phylum_taxID phylum_name class_taxID class_name order_taxID order_name family_taxID family_name subfamily_taxIsubfamily_name genus_taxID genus_name species_taxID species_name subspecies_taxID subspecies_name identification_provided_by identification_method identification_reference tax_note voucher_status tissue_type collection_event_id collectors collectiondate_start collectiondate_end collectiontime collection_note site_code sampling_protocol lifestage sex reproduction habitat associated_specimens associated_taxa extrainfo notes lat lon coord_source coord_accuracy elev depth elev_accuracy depth_accuracy country province_state region sector exactsite image_ids image_urls media_descriptors captions copyright_holders copyright_years copyright_licenses copyright_institutions photographers
CONO296-08 MNHN-IM-2007-17921 723406 MNHN_MOLL_17921 Panglao 05_96 Museum National d'Histoire Naturelle, Paris BOLD:AAD3581 23 Mollusca 92 Gastropoda 84899 Neogastropoda 866 Conidae 1900 Conus 126909 Conus orbignyi Nicolas Puillandre Audouin, 1831 MNHN/IRD FAO-71 9.49 123.74
We need to link: Specimen ID: MNHN-IM-2007-34878 / KJ550376 / AJ409610 / CONO1409-14 https://science.mnhn.fr/institution/mnhn/collection/im/item/2007-34878
http://www.boldsystems.org/index.php/Public_RecordView?processid=CONO1409-14
{
"id": "test/cae42177c14a8fcdeb14",
"scientificName": "Profundiconus maribelae",
"physicalSpecimenId": "MNHN-IM-2007-34878",
"stableIdentifier": "https://science.mnhn.fr/institution/mnhn/collection/im/item/2007-34878",
"accession": "https://identifiers.org/ena.embl:AJ409610",
"tax_id": "https://identifiers.org/taxonomy:58944"
"BIN" : "http://www.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAO3751"
}