The Big Bee network is a project to create and openly share trait information about global bees. This status page shows the current state of integration between Big Bee affiliated collections and GloBI.

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

Events

15 Sept 2021 - Formal Start of NSF funded projects related to Collaborative Research: Digitization TCN: Extending Anthophila research through image and trait digitization (Big-Bee) including NSF DBI 2102006, NSF DBI 2101929, NSF DBI 2101908, NSF DBI 2101876, NSF DBI 2101875, NSF DBI 2101851, NSF DBI 2101345, NSF DBI 2101913, NSF DBI 2101891, and , NSF DBI 2101850

8 Oct 2021 - Publication of Image Corpus: Cheadle Center for Biodiversity and Ecological Restoration, University of California Santa Barbara. (2021). UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5557670 https://archive.org/details/preston-ucsb-izc hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36

18 Oct 2021 - Big Bee poster presented by Katja Seltmann at TDWG 2021: Seltmann, K., Allen, J., Brown, B. V, Carper, A., Engel, M. S, Franz, N., et al. (2021). Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization. Biodiversity Information Science and Standards, 5(e74037). doi:10.3897/biss.5.74037 Retrieved from https://escholarship.org/uc/item/0937b5gp

28 Oct 2021 - Tara Duggan. (2021). To help fight loss of bees, California Academy of Sciences to share 180,000-strong collection online. San Francisco Chronicle. Retrieved from https://www.sfchronicle.com/climate/article/To-help-fight-loss-of-bees-California-Academy-of-16570034.php on 2 Nov 2021. tweet.

4 Nov 2021 - Publication of Image Corpus: Cheadle Center for Biodiversity and Ecological Restoration, University of California Santa Barbara. (2021). UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph (0.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5660088 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c

29 Nov 2021 - Publication of Big Bee Interaction Data: Seltmann, Katja, & Poelen, Jorrit. (2021). Tab and comma delimited versions of Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila) (v55.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5738043.

28 Jan 2022 - Publication of Big Bee Interaction Data: Seltmann, Katja, & Poelen, Jorrit. (2021). Tab and comma delimited versions of Discover Life bee species guide and world checklist (Hymenoptera: Apoidea: Anthophila) (v55.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5915003.

29 Apr 2022 - Publication of Big Bee Interaction Data: Seltmann, Katja C., & Poelen, Jorrit H. (2023). Big Bee indexed biotic interactions and review summary (0.3) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5915012.

Collections Status

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

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badge ASU / badge CAS / badge FSCA / badge MCZ / badge LACM / badge SDNHM / badge UCB / badge UCSB / badge UCM / badge KU / badge UMMZ / badge UNH /

status institution/collection platform contact
review-badge badge badge badge badge ASU / Arizona State University ASUHIC / Hasbrouck Insect Collection Symbiota Light Sangmi Lee
review-badge badge badge badge badge CAS / California Academy of Sciences ENT / Entomology Symbiota Monarch Christopher Grinter
review-badge badge badge badge badge FSCA / Florida State Collection of Arthropods / Entomology SPECIMAGE Elijah J. Talamas
review-badge badge badge badge badge MCZ / Museum of Comparative Zoology, Harvard University ENT / Entomology MCZbase-Arctos Naomi E. Pierce, Crystal Maier & Paul Morris
review-badge badge badge badge badge LACM / Natural History Museum of Los Angeles County LACMEC / Entomology KEmu Brian V. Brown & Giar-Ann Kung
review-badge badge badge badge badge SDNHM / San Diego Natural History Museum SDMC / Entomology Department Specify Pamela Horsley & Michael Wall
review-badge badge badge badge badge UCB / University of California Berkeley EMEC / Essig Museum of Entomology in-house MySQL Peter Oboyski & Neil D. Tsutsui
review-badge badge badge badge badge UCSB / University of California Santa Barbara IZC / Invertebrate Zoology Collection Symbiota Light Katja C. Seltmann
review-badge badge badge badge badge UCM / University of Colorado Museum of Natural History UCMC / Entomology Collection Specify Adrian Carper
review-badge badge badge badge badge KU / University of Kansas Natural History Museum SEMC / Entomology Division Specify Michael S. Engel & Victor H. Gonzalez
review-badge badge badge badge badge UMMZ / University of Michigan Museum of Zoology UMMZI / Division of Insects Specify L. Lacey Knowles
review-badge badge badge badge badge UNH / University of New Hampshire UNHC / Donald S. Chandler Entomological Collection TaxonWorks Istvan Miko

Integration Profiles

Integration profiles are descriptions on how data flows from one system to the next. Because the Big Bee 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

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

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.