SPNHC 2022 Data Help Desk: Difference between revisions
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=About= | =About= | ||
[[File:Spnhc-2022-data-help-desk.png|400px|right|class="w3-border w3-padding"]] | |||
For most collections professionals, a (relatively) new reality of the job is that they must manage data about specimens as well as the specimens themselves. The SPNHC 2022 Data Help Desk will provide conference attendees with an opportunity to stop by our booth and ask data-related questions in an informal and personal setting. Our local presence at the conference is paired with a concurrent virtual Data Help Desk. Our team will be happy to discuss any data-related questions or issues you may have, such as: | For most collections professionals, a (relatively) new reality of the job is that they must manage data about specimens as well as the specimens themselves. The SPNHC 2022 Data Help Desk will provide conference attendees with an opportunity to stop by our booth and ask data-related questions in an informal and personal setting. Our local presence at the conference is paired with a concurrent virtual Data Help Desk. Our team will be happy to discuss any data-related questions or issues you may have, such as: | ||
* What database / content management systems are available? | |||
* How do I get my data into a | * What database / content / collections management systems (CMS) are available? | ||
* How do I share my data with aggregators like GBIF and iDigBio? | * How do I get my data into and out of a CMS? | ||
* How do I clean my data? | * How do I share my data with biodiversity data aggregators, like GBIF and iDigBio? | ||
* How do I clean my data? Why do I need to clean my data? | |||
* What is Darwin Core, and how do I make my data Darwin Core compliant? | * What is Darwin Core, and how do I make my data Darwin Core compliant? | ||
* | * How can I utilize identifiers to enhance my data? | ||
{| class="wikitable" | {| class="wikitable" | ||
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| [https://fwbg.org/ Botanical Research Institute of Texas] | | [https://fwbg.org/ Botanical Research Institute of Texas] | ||
| | | The Fort Worth Botanic Garden and Botanical Research Institute of Texas have merged, becoming a stronger, more comprehensive botanical organization. We explore the critically important world of plants, collaborate to discover the role they play in our cultural and natural environments, and engage people to conserve nature and improve the human experience. | ||
| Jason Best | | Jason Best | ||
|- | |- | ||
| [https://www.dissco.eu/dissco-prepare/ DiSSCo Prepare] | | [https://www.dissco.eu/dissco-prepare/ DiSSCo Prepare] | ||
| | | The Distributed System of Scientific Collections (DiSSCo) is a new Research Infrastructure (RI) for Natural Science Collections that aims to create one digitally unified European collection and ensures that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding universities in the world. DiSSCo Prepare is the preparatory phase through which DiSSCo will reach the overall readiness necessary for its construction and eventual operation. | ||
| Sabine von Mering, Julia Pim Reis | | Sabine von Mering, Julia Pim Reis | ||
|- | |- | ||
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|- | |- | ||
| [http://taxonworks.org/ TaxonWorks] | | [http://taxonworks.org/ TaxonWorks] | ||
| TaxonWorks (TW) is a web-based platform serving taxonomists, biodiversity scientists, natural history collections and more. It allows you to capture, organize, and enrich your taxonomic, nomenclature, collections, and bibliographic source data; share it with collaborators; and package it for analysis and publication. The software has been in production for over 5 years and is very actively updated by a core team of 5 with numerous other community and internal contributions. Anyone in the world can and is encouraged to contribute to the open source code base, https://github.com/SpeciesFileGroup/taxonworks. Talk with us and the TW community on gitter (https://gitter.im/SpeciesFileGroup/taxonworks). | | TaxonWorks (TW) is a web-based platform, a workbench, serving taxonomists, biodiversity scientists, natural history collections and more. It allows you to capture, organize, and enrich your taxonomic, nomenclature, collections, and bibliographic source data; share it with collaborators; and package it for analysis and publication. The software has been in production for over 5 years and is very actively updated by a core team of 5 with numerous other community and internal contributions. Anyone in the world can and is encouraged to contribute to the open-source code base, https://github.com/SpeciesFileGroup/taxonworks. Talk with us and the TW community on gitter (https://gitter.im/SpeciesFileGroup/taxonworks). | ||
| [mailto:dlpaul@illinois.edu Deborah Paul] | | [mailto:dlpaul@illinois.edu Deborah Paul] | ||
|} | |} | ||
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1. '''Stop by our booth at [https://spnhc2022.com/ SPNHC 2022] in Edinburgh''' and ask a question! See the schedule of activities below. | 1. '''Stop by our booth at [https://spnhc2022.com/ SPNHC 2022] in Edinburgh''' and ask a question! See the schedule of activities below. | ||
2. '''Ask a question asynchronously via | 2. '''Ask a question asynchronously via [https://bit.ly/spnhc-2022-dhd this shared Google doc]'''. This will be live for the duration of the conference (June 5th - 10th 2022), and subsequently archived via this wiki page. | ||
3. Ask a question asynchronously via the''' ''#data-help-desk channel'' in the SPNHC Slack workspace'''. [https://join.slack.com/t/spnhc/shared_invite/zt- | 3. Ask a question asynchronously via the''' ''#data-help-desk channel'' in the SPNHC Slack workspace'''. [https://join.slack.com/t/spnhc/shared_invite/zt-19j5ema1h-bWL4WKBXT21O9HzC50LvxQ Join the SPNHC Slack here] if you haven't already! | ||
=Schedule of activities= | =Schedule of activities= | ||
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==Tools for data management== | ==Tools for data management== | ||
* '''[https://www.idigbio.org/wiki/index.php/Collections_Management_Systems Databases / Collections Management Systems (CMS)], on the iDigBio wiki''' ''note that many of these have representatives helping with the Data Help Desk! See who in the "Partners" table above, and come ask questions at our booth'' | * '''[https://www.idigbio.org/wiki/index.php/Collections_Management_Systems Databases / Collections Management Systems (CMS)], on the iDigBio wiki''' ''**note that many of these have representatives helping with the Data Help Desk! See who in the "Partners" table above, and come ask questions at our booth**'' | ||
* [https://spnhc.biowikifarm.net/wiki/Software_Resources Software Resources], on the SPNHC wiki | * [https://spnhc.biowikifarm.net/wiki/Software_Resources Software Resources], on the SPNHC wiki ''**This page is a work in progress! Want to help us populate it? Come to the "Capturing community expertise: A SPNHC wiki edit-a-thon" workshop at SPNHC on Thursday from 13:30-17:00.**'' | ||
* [https://openrefine.org/ OpenRefine], and [https://www.idigbio.org/wiki/index.php/Resources_for_using_OpenRefine Resources for using OpenRefine] | * [https://openrefine.org/ OpenRefine], and [https://www.idigbio.org/wiki/index.php/Resources_for_using_OpenRefine Resources for using OpenRefine] | ||
| Line 151: | Line 154: | ||
* [http://biodiversity-informatics-training.org/ Biodiversity Informatics Training Curriculum] | * [http://biodiversity-informatics-training.org/ Biodiversity Informatics Training Curriculum] | ||
* [https://biodiversity-specimen-data.github.io/specimen-data-use-case/ Biodiversity Specimen Data], a collection of specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions | * [https://biodiversity-specimen-data.github.io/specimen-data-use-case/ Biodiversity Specimen Data], a collection of specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions | ||
* [https://github.com/tdwg/curriculum/blob/master/biodiversity-informatics-101/bi101_schedule_2019.md Biodiversity Informatics 101], materials from a workshop at ''Biodiversity Next'' in 2019 | * [https://github.com/tdwg/curriculum/blob/master/biodiversity-informatics-101/bi101_schedule_2019.md Biodiversity Informatics 101], materials from a workshop at ''Biodiversity Next'' in 2019 | ||
Latest revision as of 08:35, 6 June 2022
About
For most collections professionals, a (relatively) new reality of the job is that they must manage data about specimens as well as the specimens themselves. The SPNHC 2022 Data Help Desk will provide conference attendees with an opportunity to stop by our booth and ask data-related questions in an informal and personal setting. Our local presence at the conference is paired with a concurrent virtual Data Help Desk. Our team will be happy to discuss any data-related questions or issues you may have, such as:
- What database / content / collections management systems (CMS) are available?
- How do I get my data into and out of a CMS?
- How do I share my data with biodiversity data aggregators, like GBIF and iDigBio?
- How do I clean my data? Why do I need to clean my data?
- What is Darwin Core, and how do I make my data Darwin Core compliant?
- How can I utilize identifiers to enhance my data?
| SPNHC 2022 Data Help Desk Partners | ||
| Organization | About | People representing |
|---|---|---|
| Arctos | Arctos is a community of museums and organizations that collaborate in the development of an online collection management information system that we consider to be fundamental research infrastructure intended for curators, collection managers, investigators, educators, and anyone interested in natural and cultural history. | Teresa J. Mayfield-Meyer |
| Biodiversity Data Standards (TDWG) | Biodiversity Information Standards (TDWG) is a not-for-profit, scientific and educational association formed to establish international collaboration among the creators, managers and users of biodiversity information and to promote the wider and more effective dissemination and sharing of knowledge about the world's heritage of biological organisms. To achieve its goals, TDWG develops, ratifies and promotes standards and guidelines for the recording and exchange of data about organisms and acts as a forum for discussing all aspects of biodiversity information management through meetings, task and interest groups, online discussions, and publications. | Deborah Paul |
| Botanical Research Institute of Texas | The Fort Worth Botanic Garden and Botanical Research Institute of Texas have merged, becoming a stronger, more comprehensive botanical organization. We explore the critically important world of plants, collaborate to discover the role they play in our cultural and natural environments, and engage people to conserve nature and improve the human experience. | Jason Best |
| DiSSCo Prepare | The Distributed System of Scientific Collections (DiSSCo) is a new Research Infrastructure (RI) for Natural Science Collections that aims to create one digitally unified European collection and ensures that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding universities in the world. DiSSCo Prepare is the preparatory phase through which DiSSCo will reach the overall readiness necessary for its construction and eventual operation. | Sabine von Mering, Julia Pim Reis |
| iDigBio | iDigBio is the central coordinating unit for the United States’ national effort to digitize natural history collections, including biological and paleontological specimens. iDigBio is a collaborative project based at the University of Florida, Florida State University, and Arizona State University that has been continuously funded by the U.S. National Science Foundation (NSF) since 2011. iDigBio’s primary goal is to catalyze excellence in digitization, mobilization, and usage of data about the biodiversity specimens curated in U.S. biodiversity collections for research and education. | Erica Krimmel, Lauren Cohen, Cat Chapman (virtually) |
| Species File Group | The Species (life on Earth) File (software) Group (collaborating community) builds tools that facilitate cataloging, description, and study of the Earth’s species. We specialize in workbenches for biodiversity scientists and indexing all the Earth's species, our group also produces a wide range of open-source libraries and utilities. Examples of work we lead and contribute to include the Catalogue of Life, Global Names Architecture, and TaxonWorks. | Deborah Paul |
| Specify Collections Consortium | The mission of the Specify Collections Consortium is to advance research and applied uses of the information associated with specimens and samples held in biological and earth science collections. With engagement and collaboration from its member institutions, the Consortium does this by engineering innovative, open-source software, and by offering training and services to members for the digitization, integration, and curation of collections data. By collaboratively creating and supporting robust platforms and tools, the Consortium advances the mobilization and engagement of collections data in broader research and computing initiatives for the benefit of its members, science, and society. | Andy Bentley (virtually) |
| Symbiota Support Hub | Symbiota is an open-source software for managing and mobilizing biodiversity data that supports a distributed network of 40+ theme-based research portals incorporating data from over 1,400 biodiversity collections. The Symbiota Support Hub (SSH) provides comprehensive services for active and developing biodiversity data portals powered by the Symbiota software platform. | Katie Pearson, Laura Prado (virtually) |
| TaxonWorks | TaxonWorks (TW) is a web-based platform, a workbench, serving taxonomists, biodiversity scientists, natural history collections and more. It allows you to capture, organize, and enrich your taxonomic, nomenclature, collections, and bibliographic source data; share it with collaborators; and package it for analysis and publication. The software has been in production for over 5 years and is very actively updated by a core team of 5 with numerous other community and internal contributions. Anyone in the world can and is encouraged to contribute to the open-source code base, https://github.com/SpeciesFileGroup/taxonworks. Talk with us and the TW community on gitter (https://gitter.im/SpeciesFileGroup/taxonworks). | Deborah Paul |
How to participate
1. Stop by our booth at SPNHC 2022 in Edinburgh and ask a question! See the schedule of activities below.
2. Ask a question asynchronously via this shared Google doc. This will be live for the duration of the conference (June 5th - 10th 2022), and subsequently archived via this wiki page.
3. Ask a question asynchronously via the #data-help-desk channel in the SPNHC Slack workspace. Join the SPNHC Slack here if you haven't already!
Schedule of activities
Please see the website for a full conference program. The table below highlights activities being organized as part of the Data Help Desk, which will take place in the conference exhibitor hall at a booth sponsored by iDigBio.
| Monday, June 6th - McEwan Hall | ||
| Time | Program | Data Help Desk Activity |
|---|---|---|
| 10:30 - 11:00 | Break | Booth staffed with data help desk partners |
| 13:00 - 14:30 | Lunch | Booth staffed with data help desk partners |
| 16:00 - 16:30 | Break | Booth staffed with data help desk partners |
| Tuesday, June 7th - McEwan Hall | ||
| Time | Program | Data Help Desk Activity |
| 09:00 - 09:30 | Pre-session | Booth staffed with data help desk partners |
| 11:00 - 11:30 | Break | Booth staffed with data help desk partners |
| 13:00 - 14:00 | Lunch | Booth staffed with data help desk partners |
| 15:30 - 16:00 | Break | Booth staffed with data help desk partners |
| Wednesday, June 7th - McEwan Hall | ||
| Time | Program | Data Help Desk Activity |
| 09:00 - 09:30 | Pre-session | Booth staffed with data help desk partners |
| 11:00 - 11:30 | Break | Booth staffed with data help desk partners |
| 13:00 - 14:00 | Lunch | Booth staffed with data help desk partners |
| 15:30 - 16:00 | Break | Booth staffed with data help desk partners |
Resources
The lists of resources below will expand based on the questions we receive from you over the course of this Data Help Desk!
Learning data skills
- DataONE Data Management Skillbuilding Hub
- ESIP Data Management Training Clearinghouse
- The Carpentries online and locally hosted courses on a variety of topics
- Introduction to Biodiversity Specimen Digitization offered by iDigBio
- Biodiversity Data Mobilization Course offered by GBIF
Planning for data management
Tools for data management
- Databases / Collections Management Systems (CMS), on the iDigBio wiki **note that many of these have representatives helping with the Data Help Desk! See who in the "Partners" table above, and come ask questions at our booth**
- Software Resources, on the SPNHC wiki **This page is a work in progress! Want to help us populate it? Come to the "Capturing community expertise: A SPNHC wiki edit-a-thon" workshop at SPNHC on Thursday from 13:30-17:00.**
- OpenRefine, and Resources for using OpenRefine
Accessing and using digital biodiversity data
- Reading data directly into your analysis script: Introduction to APIs (recorded presentation)
- Biodiversity Informatics Training Curriculum
- Biodiversity Specimen Data, a collection of specific use cases of biodiversity specimen data, documented conceptually and, where possible, linked to technical solutions
- Biodiversity Informatics 101, materials from a workshop at Biodiversity Next in 2019