| 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). | |