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== Statement of Purpose ==
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==Statement of Purpose==
  
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==Introduction==
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This page is a finding aid for users to discover information about software resources relevant to the SPNHC community. This includes but is not limited to collections/content management systems, specimen digitization tools, and tools designed to facilitate specimen-based research. Many of the resources below have been presented in SPNHC DemoCamp, a venue at the Society's annual meeting for software developers, biodiversity informaticians, digitization professionals, and collection managers to convene and share innovative approaches for the use of technology to enhance the management and use of natural history collections. See also the wiki page on [[Digitization]] for related information.
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This page is '''not''' a primary repository of information about any of the resources included in the list below. This means that no files (media or otherwise) should be uploaded to this wiki in support of the text. If in doubt, link out!
  
 
==Software Resources==
 
==Software Resources==
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The list of resources here includes both open source and proprietary software operating on both free and paid sustainability models. SPNHC does not endorse any of the resources included in the list below, and anyone is welcome to add resources that fall within the scope define in the [[#Statement of Purpose|Statement of Purpose]].
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{| class="wikitable" style="margin:auto"
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|+ style="text-align:left;" | ''Table listing software resources of interest to the natural history collections community.''
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|-
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! Name of resource
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! Developer
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! Category
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! Primary link
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! Primary point(s) of contact
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! Summary
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! Additional links
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! Links to DemoCamp presentations
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|-
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| Symbiota
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| Arizona State University
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| collections management system
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|
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|
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| 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.
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|
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|
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|-
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| TaxonWorks
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| SpeciesFile Group
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| collections management system
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|
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|
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| 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).
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|
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|-
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| Arctos
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| Arctos Consortium
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| collections management system
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|
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|
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| 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.
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|
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|
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|-
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| DiSSCo Knowledgebase
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| DiSSCo
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| knowledge base
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|
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|
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|
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|
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|
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|-
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| Global Names Architecture
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| SpeciesFile Group
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| data cleaning tool
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| https://globalnames.org/
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|
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| The Global Names Architecture (GNA) is a system of web-services which helps people to register, find, index, check and organize biological scientific names and interconnect on-line information about species.
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|
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|
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|-
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| GEOLocate
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| Yale Peabody Museum of Natural History
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| geospatial tool
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| https://www.geo-locate.org/default.html
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|
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| The GEOLocate project is an effort to develop software and services for translating textual locality descriptions associated with biodiversity collections data into geographic coordinates.
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|
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|
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|-
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| TORCH Digitization Hub
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| Botanical Research Institute of Texas
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| knowledge base
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| https://github.com/TORCH-TCN/torch_hub
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| Jason Best (jbest@brit.org), Diego Barroso (dbarroso@brit.org)
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| The Hub provides a web-based interface for managing workflows, monitoring progress and performance, and generating reports. It can be hosted in the cloud to support distributed digitization projects or hosted locally to support workflows within a single institution. While the Hub was designed for the herbarium digitization workflows of the Texas Oklahoma Regional Consortium of Herbaria (TORCH) Thematic Collections Network, it can be adapted for other types of collections and workflows and, due to its open source nature, can be extended with other image management tools and technologies such as OCR and computer vision. The TORCH Digitization Hub project code and documentation is available at https://github.com/TORCH-TCN/torch_hub.
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|
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|-
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| Conserv Cloud
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|
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| collections operations tool
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|
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|
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|
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|
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|
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|-
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| ELViS
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| SYNTHESYS+, then DiSSCo.
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| collections operations tool
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| https://elvis.dissco.eu/welcome
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|
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| This Access application portal is the first step towards the development of a European Loans and Visits system (ELViS), which will aim to provide seamless access to natural sciences collections infrastructure across Europe. This portal will be further developed to support applications for Virtual Access (digitisation), Transnational Access (visits) and loans, and to track their outcomes. After SYNTHESYS+, ELViS will be managed by the DiSSCo project.
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|
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|
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|-
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| PyrΔTE
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|
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|
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|
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|
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|
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|
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|
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|-
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| Libnova Open Access
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|
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|
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|
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|
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|
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|
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|
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|-
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| EarthCape
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|
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| collections management system
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| https://earthcape.com/
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|
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| EarthCape is a highly versatile platform for managing biodiversity research and collections data, associated molecular laboratory data, multimedia, structured ecological surveys and monitoring schemes, and more. The platform includes a fully functional Windows client as well as a web application. The data are stored in the cloud or on-premises and can be accessed by users with various access and editing rights. Routine label printing, laboratory notebook maintenance, rapid data entry set up, or any other of relatively loaded user interfaces make use of any industry standard relational database back end. This opens a wide scope for IT designers to implement desired integrations within their institutional infrastructure. APIs and developer access to core EarthCape libraries to build own applications and modules are under development. Basic data visualization (charts, pivots, dashboards), mapping (full featured desktop GIS module), data outputs (report and label designer) are tailored not only to research analyses, but also for managing logistics and communication when working on (data) papers.
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|
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|
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|-
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| IrisBG
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|
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| collections management system
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|
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|
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|
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|
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|
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|-
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| Bionomia
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|
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|
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|
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|
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|
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|
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|
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|-
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| OpenRefine
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| OpenRefine
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| data cleaning tool
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|
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|
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|
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|
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|
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|-
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|}
  
 
==Contributors==
 
==Contributors==
 +
 +
Anyone is welcome to contribute to this page! If you do, please add yourself to this list of existing contributors: [[User:Erica_Krimmel|Erica Krimmel]], Jason Best, Cat Chapman.
  
 
==References==
 
==References==

Latest revision as of 19:19, 29 May 2023

Statement of Purpose

This page is a finding aid for users to discover information about software resources relevant to the SPNHC community. This includes but is not limited to collections/content management systems, specimen digitization tools, and tools designed to facilitate specimen-based research. Many of the resources below have been presented in SPNHC DemoCamp, a venue at the Society's annual meeting for software developers, biodiversity informaticians, digitization professionals, and collection managers to convene and share innovative approaches for the use of technology to enhance the management and use of natural history collections. See also the wiki page on Digitization for related information.

This page is not a primary repository of information about any of the resources included in the list below. This means that no files (media or otherwise) should be uploaded to this wiki in support of the text. If in doubt, link out!

Software Resources

The list of resources here includes both open source and proprietary software operating on both free and paid sustainability models. SPNHC does not endorse any of the resources included in the list below, and anyone is welcome to add resources that fall within the scope define in the Statement of Purpose.

Table listing software resources of interest to the natural history collections community.
Name of resource Developer Category Primary link Primary point(s) of contact Summary Additional links Links to DemoCamp presentations
Symbiota Arizona State University collections management system 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.
TaxonWorks SpeciesFile Group collections management system 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).
Arctos Arctos Consortium collections management system 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.
DiSSCo Knowledgebase DiSSCo knowledge base
Global Names Architecture SpeciesFile Group data cleaning tool https://globalnames.org/ The Global Names Architecture (GNA) is a system of web-services which helps people to register, find, index, check and organize biological scientific names and interconnect on-line information about species.
GEOLocate Yale Peabody Museum of Natural History geospatial tool https://www.geo-locate.org/default.html The GEOLocate project is an effort to develop software and services for translating textual locality descriptions associated with biodiversity collections data into geographic coordinates.
TORCH Digitization Hub Botanical Research Institute of Texas knowledge base https://github.com/TORCH-TCN/torch_hub Jason Best (jbest@brit.org), Diego Barroso (dbarroso@brit.org) The Hub provides a web-based interface for managing workflows, monitoring progress and performance, and generating reports. It can be hosted in the cloud to support distributed digitization projects or hosted locally to support workflows within a single institution. While the Hub was designed for the herbarium digitization workflows of the Texas Oklahoma Regional Consortium of Herbaria (TORCH) Thematic Collections Network, it can be adapted for other types of collections and workflows and, due to its open source nature, can be extended with other image management tools and technologies such as OCR and computer vision. The TORCH Digitization Hub project code and documentation is available at https://github.com/TORCH-TCN/torch_hub.
Conserv Cloud collections operations tool
ELViS SYNTHESYS+, then DiSSCo. collections operations tool https://elvis.dissco.eu/welcome This Access application portal is the first step towards the development of a European Loans and Visits system (ELViS), which will aim to provide seamless access to natural sciences collections infrastructure across Europe. This portal will be further developed to support applications for Virtual Access (digitisation), Transnational Access (visits) and loans, and to track their outcomes. After SYNTHESYS+, ELViS will be managed by the DiSSCo project.
PyrΔTE
Libnova Open Access
EarthCape collections management system https://earthcape.com/ EarthCape is a highly versatile platform for managing biodiversity research and collections data, associated molecular laboratory data, multimedia, structured ecological surveys and monitoring schemes, and more. The platform includes a fully functional Windows client as well as a web application. The data are stored in the cloud or on-premises and can be accessed by users with various access and editing rights. Routine label printing, laboratory notebook maintenance, rapid data entry set up, or any other of relatively loaded user interfaces make use of any industry standard relational database back end. This opens a wide scope for IT designers to implement desired integrations within their institutional infrastructure. APIs and developer access to core EarthCape libraries to build own applications and modules are under development. Basic data visualization (charts, pivots, dashboards), mapping (full featured desktop GIS module), data outputs (report and label designer) are tailored not only to research analyses, but also for managing logistics and communication when working on (data) papers.
IrisBG collections management system
Bionomia
OpenRefine OpenRefine data cleaning tool

Contributors

Anyone is welcome to contribute to this page! If you do, please add yourself to this list of existing contributors: Erica Krimmel, Jason Best, Cat Chapman.

References

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