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Open Traits Network and
Global Biotic Interactions as a Digital Extended Specimen Use Case
Digital Data in Biodiversity Research Annual Conference
Arizona State University
2023-06-06
Jorrit H. Poelen / https://jhpoelen.nl
or
On Keeping Verifiable Digital Knowledge Available Through Collaboration, Trust and Mutual benefit
Jenn Yost asked:
1. What does a decentralized extended specimen look like?
2. What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
Jenn Yost asked:
1. What does a decentralized extended specimen look like?
2. What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
Jenn Yost
1. What is Yost's decentralized extended specimen?
2. What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
Yost's Decentralized Extended Specimen (YoDeeSpec v0.1)
Yost's Decentralized Extended Specimen (YoDeeSpec v0.1)
An ever evolving collection
Yost's Decentralized Extended Specimen (YoDeeSpec v0.1)
An ever evolving collection of particular verifiable versions
Yost's Decentralized Extended specimen (YoDeeSpec v0.1)
An ever evolving collection of particular verifiable versions of a subjective digital compilation
Yost's Decentralized Extended specimen (YoDeeSpec v0.1)
An ever evolving collection of particular verifiable versions of a subjective digital compilation of existing versioned and verifiable digital traces associated with a physical specimen
Yost's Decentralized Extended specimen (YoDeeSpec v0.1)
An ever evolving collection of particular verifiable versions of a subjective digital compilation of existing versioned and verifiable digital traces associated with a physical specimen as published by group of trusted collaborators
Yost's Decentralized Extended specimen (YoDeeSpec v0.1)
An ever evolving collection of particular verifiable versions of a subjective digital compilation of existing versioned and verifiable digital traces associated with a physical specimen as published by group of trusted collaborators enabled through mutual benefit.
Jenn Yost asked:
1. What does a decentralized extended specimen YoDeSpec v0.1 look like?
2. What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
Sea otter
Sea
otter
lunch
(c) edward_rooks, some rights reserved (CC BY-NC)
accessed at http://www.inaturalist.org/observations/563486 on Feb 4, 2015
Honey Bee
Flower
(c) Richard Barnes, some rights reserved (CC BY-NC)
accessed at http://www.inaturalist.org/observations/885255 on Oct 13, 2015
Insect
Insect's
Parasite
(c) Cheryl Harleston, some rights reserved (CC BY-NC-SA)
accessed at http://www.inaturalist.org/observations/2020957 on Oct 13, 2015
Background image: Slyusarev et al. (2015): Global Biotic Interactions food web
map. figshare. http://dx.doi.org/10.6084/m9.figshare.1297762
Global Biotic Interactions (GloBI) is a collaborative, open source, open data project that makes existing species-interaction datasets easier to discover and use.
http://globalbioticinteractions.org
1. Existing openly accessible species interaction datasets in any data format are registered using https://globalbioticinteractions.org/contribute
2. GloBI continually and automatically tracks, indexes, links, and reviews existing species interaction datasets.
3. Users discover, access and review datasets via GloBI's many integrations, search pages, data archives or APIs.
in a nutshell
Use Case:
Specimen Associations
https://globalbioticinteractions.org/process
https://globalbioticinteractions.org/process
Keep the Original Data,
Openly Share Interpretations and Reviews
Museum of Southwestern Biology, Parasite Collection (MSB:Para)
http://ipt.vertnet.org:8080/ipt/resource?r=msb_para
hash://sha256/68f846dfdef28d1b868beaa4b973e8ace40b7bc79c7c2585f21d740d60c2542c
seen at 2022-05-14T17:10:36.292Z
links to: MSB Host Collection
http://ipt.vertnet.org:8080/ipt/resource?r=msb_host
hash://sha256/4217adfb4f79af7908f52ecfd17ee23b1a41d53a33af4e11a095f00e3598d393
seen at 2022-05-14T15:35:58.134Z
Museum of Comparative Zoology
http://digir.mcz.harvard.edu/ipt/resource?r=mczbase
hash://sha256/95b55c43633eb9c5d04550add6efeef7650f82db01de59dbc04dc8ffa9bea42c
seen at 2022-05-14T16:01:30.873Z
NMNH Extant Specimen Records
https://collections.nmnh.si.edu/ipt/resource?r=nmnh_extant_dwc-a
hash://sha256/c070dfa551fa5ebf42de023ab9a976943725849e5555ae9ea2a21b950d19fab7
and many more ...
Use Case Museum of Southwestern Biology
Museum of Southwestern Biology, Parasite Collection (MSB:Para)
http://ipt.vertnet.org:8080/ipt/resource?r=msb_para
hash://sha256/68f846dfdef28d1b868beaa4b973e8ace40b7bc79c7c2585f21d740d60c2542c
seen at 2022-05-14T17:10:36.292Z
links to: MSB Host Collection
http://ipt.vertnet.org:8080/ipt/resource?r=msb_host
hash://sha256/4217adfb4f79af7908f52ecfd17ee23b1a41d53a33af4e11a095f00e3598d393
Museum of Comparative Zoology
http://digir.mcz.harvard.edu/ipt/resource?r=mczbase
hash://sha256/95b55c43633eb9c5d04550add6efeef7650f82db01de59dbc04dc8ffa9bea42c
seen at 2022-05-06T11:24:36.100Z
NMNH Extant Specimen Records
https://collections.nmnh.si.edu/ipt/resource?r=nmnh_extant_dwc-a
hash://sha256/c070dfa551fa5ebf42de023ab9a976943725849e5555ae9ea2a21b950d19fab7
and many more ...
Use Case MSB:Para:27368
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
Tetrabothrius
MSB:Para:27368
Specimen/
Individual/
Occurrence
Specimen/
Individual/
Occurrence
Nomen nescio
MCZ:Orn:348209
Study
http://arctos.database.museum/guid/MSB:Para:27368
Location
Amukta Island
Lat: 51.45166667
Lon: -171.2866667
Dataset
https://github.com/globalbioticinteractions/msb-para/archive/07743322479a0cdf1affc21c154c331dd6e84dc1.zip
collected
2002-09-01T00:00:00Z
parasite of
RO_0002444
in_dataset
collected_at
classified_as
classified_as
Simplified internal data model used by GloBI to integrate interaction data.
Flexible data model captures all kinds of interaction data.
Specimen/
Individual/
Occurrence
Specimen/
Individual/
Occurrence
Location
Amukta Island
Lat: 51.45166667
Lon: -171.2866667
parasite of
RO_0002444
collected_at
classified_as
According to Harvard MCZ https://mczbase.mcz.harvard.edu/guid/MCZ:Orn:348209
Flexible data model captures all kinds of interaction data.
Specimen/
Individual/
Occurrence
Specimen/
Individual/
Occurrence
Location
Amukta Island
Lat: 51.45166667
Lon: -171.2866667
parasite of
RO_0002444
collected_at
classified_as
According to Harvard MCZ https://mczbase.mcz.harvard.edu/guid/MCZ:Orn:348209
Flexible data model captures all kinds of interaction data.
Highlevel Parasite Description
According to Harvard MCZ https://mczbase.mcz.harvard.edu/guid/MCZ:Orn:348209
Flexible data model captures all kinds of interaction data.
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
According to Arctos http://arctos.database.museum/guid/MSB:Para:27368
Flexible data model captures all kinds of interaction data.
GloBI Web Interface
https://globalbioticinteractions.org/?accordingTo=http%3A%2F%2Farctos.database.museum%2Fguid%2FMSB%3APara%3A27368 in June 2022
Flexible data model captures all kinds of interaction data.
Tetrabothrius
MSB:Para:27368
Specimen/
Individual/
Occurrence
Specimen/
Individual/
Occurrence
Black-legged Kittiwake
(Rissa tridactyla)
MCZ:Orn:348209
Study
http://arctos.database.museum/guid/MSB:Para:27368
Location
Amukta Island
Lat: 51.45166667
Lon: -171.2866667
Dataset
https://github.com/globalbioticinteractions/msb-para/archive/07743322479a0cdf1affc21c154c331dd6e84dc1.zip
collected
2002-09-01T00:00:00Z
parasite of
RO_0002444
in_dataset
collected_at
classified_as
classified_as
Simplified internal data model used by GloBI to integrate interaction data.
Extended
Linked/ Extended
Flexible data model captures all kinds of interaction data.
GloBI Web Interface
https://globalbioticinteractions.org/?accordingTo=http%3A%2F%2Farctos.database.museum%2Fguid%2FMSB%3APara%3A27368 in June 2023
Flexible data model captures all kinds of interaction data.
linking all the data
Bidirectional links include Encyclopedia of Life, Gulf of Mexico Species Interactions, NCBI Taxonomy, World Register of Marine Species, iNaturalist, Fishbase, SeaLifeBase, and Arctos, and more.
Outgoing links include UBERON (body parts, life stage, physiological state), EnvO, GeoNames, CMECS, FEOW, MEOW, TEOW, doi.org, ITIS, Open Tree of Life, NBN and ALA.
Link services include Global Names and CrossRef.
Figure from http://globalbioticinteractions.org/2016/02/08/ecology-of-data/ accessed at 28 Sept 2017
linking all the data
and their curators
Bidirectional links include Encyclopedia of Life, Gulf of Mexico Species Interactions, NCBI Taxonomy, World Register of Marine Species, iNaturalist, Fishbase, SeaLifeBase, and Arctos
Outgoing links include UBERON (body parts, life stage, physiological state), EnvO, GeoNames, CMECS, FEOW, MEOW, TEOW, doi.org, ITIS, Open Tree of Life, NBN and ALA.
Link services include Global Names and CrossRef.
Figure from http://globalbioticinteractions.org/2016/02/08/ecology-of-data/ accessed at 28 Sept 2017
Fig 2. from Gallagher et al. 2022. Nat Ecol Evol doi:10.1038/s41559-020-1167-9.
Open Traits Network
it takes a village
to keep and share
a record
Fig 1. from Keller et al. 2022 Methods in Ecol and Evol doi:10.1111/2041-210X.14033
Jenn Yost asked:
1. What does a decentralized extended specimen (YoDeeSpec v0.1) look like?
2. What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
What roadblocks did he encounter when building this resource, and what is still needed to better combine the data?
Time, and time & elbow grease.
Jorrit is wondering:
1. What does a decentralized extended specimen look like to you?
2. What roadblocks did you encounter when building this resource, and what is still needed to better combine the data?
partners
Acknowledgments
an incomplete list in no particular order
These projects would not have been possible without the many contributions (big and small) of folks like Jen Hammock, Katja Schulz, Pepper Luboff, Chris Mungall, Katja Seltmann, Brian Hayden, Ken-ichi Ueda, Jim Simons, Theresa Mitchell, Emanuel Heitlinger, Kathy Kwan, Deng Palomares, Josephine “Skit” Barile, Anne Thessen, Allen Hurlbert, Dmitri Mozzherin, Malcolm Storey, Michael Elliott, José Fortes, Quentin Groom, Nathan Upham, Deb Paul, Mariya Dimitrova, Lyubomir Penev, Donat Agosti, Alex Ioannidis, Marcus Guidoti, Jen Zaspel, Carl Boettiger, Erika Tucker … and thousands of others that have collected and shared biodiversity data and related tools.
Jorrit Poelen @ https://jhpoelen.nl
Thank you!
Works presented are funded in part by grants OAC 1839201, DBI 1901932, DBI 1901926, DBI 2102006 from the National Science Foundation, 1-R21-AI164268-01 from the National Institutes of Health, the Encyclopedia of Life Rubenstein Fellows Program (CRDF EOL-33066-13/F33066, 2013), EOL David M. Rubenstein Grant (FOCX-14-60988-1, 2014), and the Smithsonian Institution (SI) (T15CC10297-002, 2016).
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