Terrestrial Parasite Tracker

This Terrestrial Parasite Tracker (TPT) status page shows the current state of integration between TPT affiliated collections and GloBI.

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events / collections status / integration profiles / DwC-A guidelines / translation tables / supported biotic interaction terms

Events

1 Oct 2019 - Parasite Tracker kick-off presentation / video.

24 Feb 2020 - Publication of Poelen, Jorrit H., Seltmann, Katja & Campbell, Mariel. (2020). Terrestrial Parasite Tracker indexed biotic interactions and review summary (Version 0.1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3685365 . For summaries see indexed_interactions_by_collection.tsv and review_summary_by_collection.tsv. For full report with review comments, indexed interactions and source datasets, please visit the Zenodo data publication at http://doi.org/10.5281/zenodo.3685365.

5 Mar 2020 - workshop GloBI presentation available via doi:10.17605/OSF.IO/VK8WQ, workshop blog post at Tracking Parasites

30 April 2020 - Publication of Poelen, Jorrit H., Seltmann, Katja C., & Campbell, Mariel. (2020). Terrestrial Parasite Tracker indexed biotic interactions and review summary (Version 0.2) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3778773 . For summaries see indexed_interactions_by_collection.tsv and review_summary_by_collection.tsv. For full report with review comments, indexed interactions and source datasets, please visit the Zenodo data publication at http://doi.org/10.5281/zenodo.3778773.

1 May 2020 - Publication of Kathryn Sullivan, Katja Seltmann, Jorrit Poelen, & Jennifer M. Zaspel. (2020, May). Making Parasite-Host Associations Visible in Terrestrial Parasite Tracker (TPT) (Version 0.0.1). Zenodo. http://doi.org/10.5281/zenodo.3780543. The publication (see doi:10.5281/zenodo.3780543) contains transcription guidelines to help capture biotic assocations in natural history collections.

8 July 2020 - Webinar: Making parasite-host associations visible in Terrestrial Parasite Tracker (TPT) mp4 video / slides / iDigBio wiki. The slides have been published via on update of: Kathryn Sullivan, Katja Seltmann, Jorrit Poelen, & Jennifer M. Zaspel. (2020, May). Making Parasite-Host Associations Visible in Terrestrial Parasite Tracker (TPT) (Version 0.0.1). Zenodo. http://doi.org/10.5281/zenodo.3941952 .

TPT Collections Status

Click on badges to browse/download indexed records or inspect automated reviews.

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badge BPBM / badge BYU / badge CAS / badge CUAC / badge FMNH / badge INHS / badge MSU / badge MPM / badge HWML / badge OSAL / badge PSUC / badge PU / badge TAMUIC / badge BRTC / badge ANSP / badge USNM / badge UCSB / badge UHIM / badge UMMZ / badge UMSP / badge UNHC / badge MSB / badge MSB / badge UTAH / badge WIRC / badge UWSP / badge VB / badge YPM /

status institution/collection platform contact
review-badge index-badge badge BPBM / Bishop Museum / J. Linsley Gressitt Center for Research in Entomology Specify Jim Boone, Neal Evenhuis
review-badge index-badge badge BYU / Brigham Young University Arthropod Museum BYUC / Monte L. Bean Museum of Life Science Museum Insects and Arachnids SymbSCAN Michael Whiting
review-badge index-badge badge CAS / California Academy of Sciences / Entomology Collection Institutional Chris Grinter, Michelle Trautwein
review-badge index-badge badge CUAC / Clemson University / Clemson University Arthropod Collection Specify Michael Caterino
review-badge index-badge badge FMNH / Field Museum of Natural History / FMNH Insects, Arachnids, and Myriapods EMu John Bates, Maureen Turcatel, Petra Sierwald
review-badge index-badge badge INHS / Illinois Natural History Survey, University of Illinois at Urbana-Champaign / INHS Insect Collection TaxonWorks Dmitry A Dmitriev, Matt Yoder
review-badge index-badge badge MSU / Michigan State University MSUC / Albert J. Cook Arthropod Research Collection SymbSCAN Anthony Cognato, Sarah Smith
review-badge index-badge badge MPM / Milwaukee Public Museum / MPM Zoology EMu Kat Sullivan, Alyssa Caywood, Christopher Tyrrell, Jennifer Zaspel , Julia Colby
review-badge index-badge badge HWML / Nebraska State Museum / Harold W. Manter Laboratory of Parasitology Arctos Scott Gardner
review-badge index-badge badge OSAL / Ohio State University / Ohio State University Acarology Collection Filemaker Pro Hans Klompen
review-badge index-badge badge PSUC / Pennsylvania State University ENTO / Frost Entomological Museum TaxonWorks Andy Deans, Joyce Sakamoto, Laura Porturas
review-badge index-badge badge PU / Purdue University PERC / Entomological Research Collection Specify Jessica Williams, Stephen Cameron
review-badge index-badge badge TAMUIC / Texas A&M University / Texas A&M University Insect Collection SQL Server John Oswald, Karen Wright
review-badge index-badge badge BRTC / Texas A&M University / Biodiversity Teaching and Research Collections Access Jessica Light
review-badge index-badge badge ANSP / The Academy of Natural Sciences of Drexel University / Ornithology Collection at Academy of Natural Sciences of Drexel University SymbSCAN Jason Weckstein
review-badge index-badge badge USNM / United States National Museum of Natural History (USNM), Smithsonian Institution USNMENTFLEA / United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU) Institutional David Pecor
review-badge index-badge badge UCSB / University of California at Santa Barbara IZC / Invertebrate Zoology Collection Symbiota Katja Seltmann
review-badge index-badge badge UHIM / University of Hawaii Insect Museum UHIM / University of Hawaii Insect Museum SymbSCAN Daniel Rubinoff
review-badge index-badge badge UMMZ / University of Michigan Museum of Zoology / University of Michigan Museum of Zoology Insect Collection Specify Barry OConnor, Erika Tucker
review-badge index-badge badge UMSP / University of Minnesota / University of Minnesota Insect Collection Specify Ralph Holzenthal, Robin Thomson
review-badge index-badge badge UNHC / University of New Hampshire / UNH Collection of Insects and other Arachnids Filemaker Pro Istvan Miko
review-badge index-badge badge MSB / University of New Mexico PARA / Museum of Southwestern Biology, Divisions of Mammals, Parasites Arctos Mariel Lee Campbell, Joseph Cook
review-badge index-badge badge MSB / University of New Mexico HOST / Museum of Southwestern Biology, Host Collection Arctos Mariel Lee Campbell, Joseph Cook
review-badge index-badge badge UTAH / University of Utah PIPER / Price Institute of Parasites Research (PIPeR) SymbSCAN Sarah Bush
review-badge index-badge badge WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection Specify Craig Brabant, Daniel Young
review-badge index-badge badge UWSP / University of Wisconsin Stevens Point PARA / Stephen J. Taft Parasitological Collection SymbSCAN Sarah Orlofske
review-badge index-badge badge VB / VectorBase / Institutional Samuel Rund
review-badge index-badge badge YPM / Yale Peabody Museum (YPM) / Yale Peabody Museum EMu Larry Gall

Integration Profiles

Integration profiles are descriptions on how data flows from one system to the next. Because the Parasite Tracker community is using a variety of tools (e.g., Arctos, Symbiota, Specify, Excel, MSAccess) to manage and share collection data, there are many integration profiles to exchange collection data. The integration profiles below are geared towards the exchange and linking of biotic associations data (e.g., species interactions, or host-parasite associations) with GloBI.

Arctos

Arctos managed collections are indexed by GloBI. This section explains how.

Arctos GloBI Integration Profile
authors Dusty (Arctos dev), Mariel Campbell (MSB), Teresa Mayfield-Meyer (MSB)
actors Arctos, VertNet, GloBI
integration method A collection manager uses Arctos to establish associations or relationships between records. Arctos periodically shares data with VertNet. VertNet uses GBIF IPT software to publish data archives. VertNet publishes a list of available datasets in the form of a RSS feed, including those shared by Arctos. Periodically, GloBI finds, and downloads, Arctos related data archives in VertNet. Then, GloBI indexes the associatedOccurrences fields of records in these Arctos data archives. The associatedOccurrences contain the association type (e.g., “eats”) and a pointer to the occurrence id of the linked record.
diagram arctos-integration.png
example collection MSB-PARA

Symbiota

SymbSCAN

Various Symbiota-based collections are indexed by GloBI. This section explains how.

Symbiota GloBI Integration Profile
authors Katja Seltmann (UCSB)
actors Collection Manager, Symbiota CMS1, Symbiota Portal1, GloBI
integration method A collection manager uses the “associatedTaxa” fields in Symbiota CMS to record host-parasite associations. The Symbiota CMS periodically publishes their data to a Symbiota Portal (e.g., https://scan-bugs.org , ) . After successful publication, the Symbiota Portal includes the updates data archive in their list of available datasets through their RSS feed. GloBI indexes all data archives in the list of available datasets. For each dataset, GloBI looks for association records in associatedTaxa, associatedOccurrences, dynamicProperties field as well as Resource Relationship and Associated Taxa Extensions. In this case, only associatedTaxa fields are encountered and related records are indexed accordingly.
diagram symbiota-integration.png
example collection UCSB-IZC

1Note that Symbiota includes two distinct systems: Symbiota CMS and Symbiota Portal. Symbiota CMS is a collection management system typically used to keep a digital inventory of physical collections. Symbiota Portal exposes digital records as Darwin Core Archives and Ecological Metadata Language files, These Darwin Core Archives and EML files are included in a list of available datasets in the form of a RSS feed. So, This include records retrieved from Symbiota CMS as well as other systems or datasources (e.g., spreadsheets, csv files). Symbiota Portal is used to help interface with national and global aggregators like iDigBio and GBIF.

Specify

Association records in Specify managed collections are indexed by GloBI. This section explains how.

Specify GloBI Integration Profile
authors Ralph Holzenthal (UMSP), Robin Thomson (UMSP)
actors Collection Manager, Excel, Specify6, https://scan-bugs.org
integration method Collection Manager enters records in excel, then uploads the records in batch into Specify. A manual export to https://scan-bugs.org is done periodically to provide updates to GBIF, iDigBio and GloBI. If updates are made to existing Specify records, a new batch export is needed to update https://scan-bugs.org .
diagram specify-integration.png
example collection  
open questions 1. Which darwin core archive field to use for assocations? associatedTaxa, associatedOccurrences, Resource Relationship extension. 2. Can we automate the export of Specify records to SCAN?
references Linking Specify data to SCAN Collection Provided by Laura Prado, U. of Wisconsin (December 8, 2018) https://scan-all-bugs.org/?page_id=2084
Specify GloBI Integration Profile
authors Erika Tucker (UMMZ), Barry Oconner (UMMZ)
actors Collection Manager, Specify, https://gbif.org/
integration method Collection Manager enters records in Specify. A manual csv export of full Specify database (including host records) is shared with, and indexed by, GloBI. If updates are made to existing Specify records, a manual export performed and GloBI is notified.
diagram specify-integration-ummzi.png
example collection  
open questions 1. Which darwin core archive field to use for assocations? associatedTaxa, associatedOccurrences, Resource Relationship extension. 2. How to establish an automated the export of Specify records via (UMich) IPT? 3. How to best link to individual specimen records? 4. How to best cite specimen records? 5. How to establish reliable links to non-UMMZI host records?
references 2020-01-23 Meeting notes and Jan 2020 email exchanges between Jorrit (GloBI), Erika (UMMZ), Barry (UMMZ)
example collection UMMZ, UMMZI on GloBI and UMMZI on github .

EMu

The EMu <> GloBI integration profiles describes a way GloBI indexes assocation data originating from EMu .

EMu/GBIF GloBI Integration Profile
authors Kate Webbink, Janeen Jones
actors FMNH Collection Manager, EMu, IPT, GloBI
integration method A collection manager uses EMu to establish associations or relationships between Catalogue (occurrence) records. The collection manager periodically exports datasets from EMu, and the IT Department publishes those datasets as resources on the FMNH IPT - fmipt.fieldmuseum.org. Datasets (“IPT resources”) that include interactions among occurrences will include a Darwin Core “Resource Relationship” extension. The fmipt site publishes a list of available IPT resources in the form of a RSS feed (https://fmipt.fieldmuseum.org/ipt/rss.do), similarly to VertNet. Periodically, GloBI could find and download FMNH-related data archives in the fmipt. Then, GloBI could index the resourceID fields of records in these FMNH data archives (IPT resources). The relationshipOfResource field contains the relationship type (e.g., “stomach contents of”) and the relatedResourceID field contains a pointer to the occurrenceID of the linked record.
diagram A workflow using a public EMu website for GloBI to link back into: emu-integration.svg An alternative workflow using a Symbiota Portal for public linking: emu-mpm-integration.svg
example collection https://fmipt.fieldmuseum.org/ipt/manage/resource?r=fmnh-rr-test ( https://github.com/jhpoelen/eol-globi-data/files/3586074/dwca-fmnh-rr-test-v1.1.zip ) Post-FMNH/EMu-data-standardization, more resources on fmipt will include a “Resource Relationship” DwC extension

TAMUIC

TAMUIC GloBI Integration Profile
authors John Oswald
actors Collection Manager, SQL Server, SCAN, GloBI
integration method A collection manager uses SQL Server to manage collection record relations. The collection manager episodically exports datasets from SQL Server to SCAN as a Darwin Core Archive. Periodically, GloBI indexes TAMUIC related datasets as part of indexing all of SCAN.
diagram tamuic-integration.png

TaxonWorks

PSUC GloBI Integration Profile
authors Andrew R. Deans, Laura Porturas
actors Curator, Data Manager, TaxonWorks, SCAN, GloBI
integration method A curator uses TaxonWorks to manage collection object associations. The data manager periodically exports data from TaxonWorks to SCAN as Darwin Core Archive. Periodically, GloBI indexes PSUC datasets as part of indexing all of SCAN.
diagram ?
example collection ?

Institutional

Undecided

Your platform/project here GloBI Integration Profile
authors ?
actors ?
integration method ?
diagram ?
example collection ?

Aside from various collection management systems, some collections use custom, home grown tools to manage their digital inventory. When feasible, we aim to develop custom integration profiles for those institutional solutions, provided that the data is openly accessible on the internet.

DwCA Guidelines

Darwin Core Archives provide several ways to capture biotic associations including: associatedTaxa, associatedOccurrences, ResourceRelationship, and dynamicProperties.

For specific examples also see GloBI blog posts Associating with Natural History Collections and Models in Fashion.

General Guidelines

The interaction information should be shared in multiple ways through DwC-A because no single way is sufficient for all aggregators. GBIf does display Dynamic Properties and Associated Taxa (according to K. Seltmann).

Associated Taxa

http://rs.tdwg.org/dwc/terms/associatedTaxa should always be filled out when an association is present (according to K. Seltmann).

Associated Occurrences

If http://rs.tdwg.org/dwc/terms/associatedOccurrences are listed, those should be a separate column in the DwC-A (not included in http://rs.tdwg.org/dwc/terms/dynamicProperties) (according to K. Seltmann).

http://rs.tdwg.org/dwc/terms/associatedOrganisms may include a relationship and link.

Dynamic Properties

http://rs.tdwg.org/dwc/terms/dynamicProperties should be used to handle all other information about an interaction formatted in JSON (according to K. Seltmann).

Resource Relations

https://dwc.tdwg.org/terms/#resourcerelationship is another way of adding biotic interactions to the Darwin Core archive, but only accommodates key:values, thus dynamicProperties will also be needed for more complex information (according to K. Seltmann).

https://dwc.tdwg.org/terms/#resourcerelationship is designed to link, or relate, occurrence/taxon or any kind of DwC record using a defined relationship. This means that many details from the linked records are inherited (e.g., lifestage of a specimen described by a linked occurrence record). However, limited information (e.g., https://dwc.tdwg.org/terms/#dwc:relationshipAccordingTo, https://dwc.tdwg.org/terms/#dwc:relationshipEstablishedDate, https://dwc.tdwg.org/terms/#dwc:relationshipRemarks) can be associated to the relationship record itself (according to J.H. Poelen).

(work in progress) Include best practices, pros/cons, examples and links to datasets using the extensions.

Interaction Types

Supported Terms

Translation Tables

GloBI uses a subset of biotic interaction (or association) terms defined in the OBO Relations Ontology (OBO RO) to help classify and index biotic associations in collection records. Verbatim association types (e.g., on, parasite of, found on) are explicitly mapped into these OBO RO terms using translation tables. GloBI keeps a default translation tables and specific collection may choose to provide their own (see e.g., INHS-Insects ).

resource description
OBO Relations Ontology project page OBO RO contains many kinds of terms, not just biotic associations terms
List of OBO RO Biotic Interaction Terms with definitions a table of RO biotic interaction terms and their definitions (if available)
List of GloBI Supported Interaction Terms subset of RO interactions terms that GloBI uses for indexing
Default Verbatim Terms Translation Table the translation table used by GloBI to maps verbatim interaction terms to supported interaction terms
Example of Custom Verbatim Terms Translation Table if provided/needed, GloBI can use a custom mapping provided by a collection

The OBO RO is far from complete and we expect to add new terms and improve definitions as needed. Also, GloBI translation tables can be easily updated when needed. Please open an issue if you have questions or suggestions.