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).