Difference between revisions of "IIIF"

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== Implementation of IIIF for Natural History Collections ==
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= Implementation of IIIF for Natural History Collections =
  
 
The CETAF Identifier specification provides a uniform way for people and machines to access textual data about specimens over the internet but one of the primary use cases is to access images of specimens. These pages document best practice for exposing specimen images using IIIF and why this approach is recommended. The initial development of these recommendations was carried out as part of an EU funded Synthesys+ Task 4.3 (2019-2021) which was part of the larger [https://www.dissco.eu/ DISSCo] initiative.
 
The CETAF Identifier specification provides a uniform way for people and machines to access textual data about specimens over the internet but one of the primary use cases is to access images of specimens. These pages document best practice for exposing specimen images using IIIF and why this approach is recommended. The initial development of these recommendations was carried out as part of an EU funded Synthesys+ Task 4.3 (2019-2021) which was part of the larger [https://www.dissco.eu/ DISSCo] initiative.
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IIIF ([[https://iiif.io/ International Image Interoperability Framework]]) is an exchange standard for sharing multimedia representations of objects on-line. It has been adopted by many institutions and commercial partners in the digital humanities community but, before Synthesys+ Task 4.3, was not used in the Natural History community.
 
IIIF ([[https://iiif.io/ International Image Interoperability Framework]]) is an exchange standard for sharing multimedia representations of objects on-line. It has been adopted by many institutions and commercial partners in the digital humanities community but, before Synthesys+ Task 4.3, was not used in the Natural History community.
  
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== Background ==
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There is quite a lot of information here so it is split across multiple pages.
  
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Researchers have become accustomed to online access to data about the specimens held in natural history collections. Over several decades metadata standards have been developed to facilitate the sharing and aggregation of these data, notably [https://www.tdwg.org/standards/dwc/ Darwin Core] and [https://www.tdwg.org/standards/abcd/ ABCD] (Access to Biological Collections Data) developed under the auspices of the Biodiversity Information Standards organization ([https://www.tdwg.org/ TDWG]) but other standards developed in other communities, have also proved useful, notably [https://eml.ecoinformatics.org/ EML] (Ecological Metadata Language) from the Ecological Society of America and Long Term Ecological Research Network, and [https://www.ogc.org/standards/gml GML] (Geography Markup Language) from the Open Geospatial Consortium ([https://www.ogc.org/ OGC]).
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== Introduction ==
  
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Data aggregators have arisen who both drive standards development and take advantage of the vast number of records made available through this community effort. Examples include [https://www.ala.org.au/ Atlas of Living Australia], [https://eol.org/ EoL] (Encyclopedia of Life), [https://www.idigbio.org/ iDigBio], [https://gbif.org/ GBIF] (Global Biodiversity Information Facility) and [http://www.worldfloraonline.org/ WFO] (World Flora Online). Aggregators with a wider cultural scope have also shown an interest in representing natural history material, notably [https://www.jstor.org/ JSTOR] and [https://www.europeana.eu/ Europeana].
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* [[IIIF Background]] - Why IIIF looks like the right fit for Natural History Specimens.
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* [[IIIF Framework]] - An overview of the IIIF Framework including the standards and organisation.
  
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In addition to these successes there are still many “dark specimens” that are not visible to the web and efforts continue to digitise data on these objects and expose it online.
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== Linking ==
  
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The vast majority of the data that have been liberated so far have therefore been text based data about specimens and the exchange standards reflect this. But many institutions and projects have simultaneously been imaging their specimens, producing large numbers of images and other media associated with their specimens that they want researchers to be able to access.
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* [[IIIF Linking HTML]] - How to link to and from a IIIF Manifest and a HTML page.
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* [[IIIF Linking CETAF IDs]] - How to link to and from a IIIF Manifest and CETAF ID.
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* [[IIIF Linking Darwin Core]] - How to link from Darwin Core Archive files to IIIF Manifests
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* [[IIIF Linking ABCD]] - How to link from ABCD metadata to a IIIF Manifest
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* [[IIIF Linking CSV]] - Linking from generic CSV download files.
  
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Some existing standards have created media extensions to accommodate the sharing of images and other multimedia formats. However, these are restricted to metadata about media objects rather than the exchange of the media objects themselves. For example, two extensions to Darwin Core are [https://tdwg.github.io/ac/introduction/ Audubon Core], (Multimedia Resources Task Group 2013) which is designed to “determine whether a particular resource or collection will be fit for some particular biodiversity science application before acquiring the media.” and the [https://tools.gbif.org/dwca-validator/extension.do?id=gbif:Multimedia Simple Multimedia extension], which is a “simple extension for exchanging metadata about multimedia resources”. Therefore image exchange, in particular, has not used open standards. Projects have relied on transferring high resolution versions of images (e.g. submission of type specimen images to JSTOR) or cut down compressed versions (e.g. many herbarium specimens submitted to The Global Biodiversity Information Facility (GBIF) or to Europeana).
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== Deployments ==
  
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The ''ad hoc'' network of institutions, organisations and projects that has emerged has not allowed access to high resolution versions of images as curated by the host institutions themselves beyond basic links to web pages. If high resolution images have been published in online catalogues, they have been made available using a hotchpotch of different technologies including the now defunct Java Applets and Adobe Flash player. The network has not supported different views of the same specimen or annotations of those views, or integration of audio and moving images.
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=== Case Studies ===
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* [[IIIF RBGE Example]] - How IIIF is implemented at the Royal Botanic Garden Edinburgh (E)
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* [[IIIF Herbaria Mundi]] - An example of combining IIIF resources from multiple sources
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* [[IIIF BGBM Example]] - How IIIF is implemented at the Botanic Garden and Botanical Museum Berlin (B)
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* [[IIIF MfN Example]] - How IIIF is implemented at Museum für Naturkunde Berlin
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* [[IIIF Meise Example]] - How IIIF is implemented at Meise Botanic Garden
  
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Natural history collections are not isolated from each other. Most research has to be conducted across collections, because in most cases no one collection holds all the specimens on a taxon. Furthermore, there are many implicit and explicit links between collections. For example, botanical specimens are frequently created in duplicate and distributed to multiple herbaria . In an ideal world a researcher should be able to view and annotate images of specimens held across multiple collections in a unified way, and the host institutions should have access to those annotations and statistics on how their specimens are being used. It should be as if the researcher had the specimens in their hands. How can we achieve this? How can we reduce the barrier to access created by history and geography? This also speaks to the Article 17 of the Convention on Biological Diversity on exchange of information. It states that:
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=== Installations ===
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==== Royal Botanic Garden Edinburgh (E) ====
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* Status: IIIF end point in production.
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* Example CETAF ID: https://data.rbge.org.uk/herb/E00008781
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* Example IIIF Manifest: https://iiif.rbge.org.uk/herb/iiif/E00008781/manifest
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==== Botanic Garden and Botanical Museum Berlin (B) ====
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* Status: IIIF end point in production.
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* Example CETAF ID: https://herbarium.bgbm.org/object/B200012401
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* Example IIIF Manifest: https://herbarium.bgbm.org/data/iiif/B200012401/manifest.json
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==== Museum für Naturkunde Berlin (MfN) ====
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* Status: IIIF end point in production.
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* Developers actively contributing to IIIF viewer code bases.
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* Example CETAF ID: https://portal.museumfuernaturkunde.berlin/detail/a3293da550fafbcd706e
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* Example IIIF Manifest: https://portal.museumfuernaturkunde.berlin/api/v1/iiif/manifest/a3293da550fafbcd706e/manifest.json
  
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<blockquote>
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==== Meise Botanic Gardens ====
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“The Contracting Parties shall facilitate the exchange of information, from all publicly available sources, relevant to the conservation and sustainable use of biological diversity, taking into account the special needs of developing countries”.
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* Status: IIIF end point in production.
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</blockquote>
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* Example CETAF ID: https://www.botanicalcollections.be/specimen/BR0000022705044
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* Example IIIF Manifest: http://iiif-manifest.oxalis.br.fgov.be/specimen/BR0000022705044/manifest
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Clearly, facilitating access to high quality images of biological specimens across the internet would at least partially resolve barriers to research in some of the most biodiverse countries.
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==== Asociación Jardín Botánico La Laguna (LAGU) ====
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* Status: IIIF in production.
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The notion of sharing and annotating specimen images is not new to the natural history community. [https://www.morphbank.net/ MorphBank], founded in 1998, has grown to allow much of this desirable functionality but at the cost and fragility of being a centralised database. The question we should perhaps be asking is: how can we make the biodiversity data sharing network as a whole more like MorphBank?
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* Example CETAF ID: http://lagu.jacq.org/object/PG-03584
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* Example IIIF Manifest: http://lagu.jacq.org/iiif/PG-03584 
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The sharing of multimedia representations of objects online is not a problem unique to the biodiversity community. Scholars in museums and archives of all kinds are facing the same issues. In 2011 the [https://www.bl.uk/ British Library], [https://www.stanford.edu/ Stanford University], the [https://www.bodleian.ox.ac.uk/ Bodleian Libraries] (Oxford University), the [https://www.bnf.fr/en Bibliothèque nationale de France, Nasjonalbiblioteket] (National Library of Norway), [https://www.lanl.gov/library/ Los Alamos National Laboratory Research Library], and [https://www.cornell.edu/ Cornell University] came together to develop an exchange standard called IIIF (International Image Interoperability Framework - pronounced “Triple-Eye-Eff”). This framework now consists of six APIs (Application Programming Interface), five stable and one in beta, to publish and integrate image and other multimedia resources in a uniform manner. It has been adopted by many institutions and commercial partners in the digital humanities. Applications based on IIIF enable many of the features desired by biodiversity researchers.
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==== Institute of Botany, Ilia State University (TBI) ====
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* Status: IIIF in production.
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These wiki pages are based on a document which was the culmination of an international project (Synthesys+ Task 4.3) funded by the European Commission that has run from 2019 to 2021. The purpose of Synthesys+ Task 4.3 was to encourage the use of IIIF as a standard way of sharing images of natural history objects and to link this to the CETAF specimen IDs already in use. The task did this by establishing exemplar implementations (subtask 4.3.1) and documenting our experiences in the form of a document to apply IIIF to other collections (subtasks 4.3.2 and 4.3.3).
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* Example CETAF ID: http://tbi.jacq.org/object/TBI1038592
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* Example IIIF Manifest: http://tbi.jacq.org/iiif/TBI1038592
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==== Herbarium Rita & Eckhard Willing Herbarium ====
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* Status: IIIF end point in production.
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* Example CETAF ID: https://willing.jacq.org/object/JACQID1184346
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* Example IIIF Manifest: http://willing.jacq.org/iiif/JACQID1184346
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==== Finish Museum of Natural History (Luomus) ====
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* Status: IIIF near production. Image API in place Presentation API to follow.
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* Example CETAF ID: http://id.luomus.fi/KN.17856
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* Example IIIF Image: https://iiif-laji.rahtiapp.fi/iiif/3/MM.1619624/info.json
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==== University of Leipzig, Herbarium (LZ) ====
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* Status: IIIF in production.
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* Example CETAF ID: https://lz.jacq.org/LZ012400
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* Example manifest: https://sammlungen-editor.uni-leipzig.de/api/iiif/presentation/v2/ULBotanyHerbarium_derivate_00003357/manifest
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==== NHM Vienna (W) ====
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* Status: Cantaloupe and IIPSrv are setup in a testbed Mirador vs. UniverslViewer are evaluated and final decision on server and viewer before Q4 2022.
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* Example CETAF ID: https://w.jacq.org/W0100330
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==== University of Vienna, Herbarium (WU) ====
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* Status: IIIF in production.
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* Example CETAF ID: https://wu.jacq.org/WU0044029
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* Example combined manifest: Image and CMS JACQ "Metadata" https://services.jacq.org/jacq-services/rest/iiif/manifest/142213
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* Example image manifest: https://app05a.phaidra.org/manifests/WU0044029

Latest revision as of 06:21, 13 October 2022

Implementation of IIIF for Natural History Collections

The CETAF Identifier specification provides a uniform way for people and machines to access textual data about specimens over the internet but one of the primary use cases is to access images of specimens. These pages document best practice for exposing specimen images using IIIF and why this approach is recommended. The initial development of these recommendations was carried out as part of an EU funded Synthesys+ Task 4.3 (2019-2021) which was part of the larger DISSCo initiative.

IIIF ([International Image Interoperability Framework]) is an exchange standard for sharing multimedia representations of objects on-line. It has been adopted by many institutions and commercial partners in the digital humanities community but, before Synthesys+ Task 4.3, was not used in the Natural History community.

There is quite a lot of information here so it is split across multiple pages.

Introduction

  • IIIF Background - Why IIIF looks like the right fit for Natural History Specimens.
  • IIIF Framework - An overview of the IIIF Framework including the standards and organisation.

Linking

Deployments

Case Studies

Installations

Royal Botanic Garden Edinburgh (E)

Botanic Garden and Botanical Museum Berlin (B)

Museum für Naturkunde Berlin (MfN)

Meise Botanic Gardens

Asociación Jardín Botánico La Laguna (LAGU)

Institute of Botany, Ilia State University (TBI)

Herbarium Rita & Eckhard Willing Herbarium

Finish Museum of Natural History (Luomus)

University of Leipzig, Herbarium (LZ)

NHM Vienna (W)

  • Status: Cantaloupe and IIPSrv are setup in a testbed Mirador vs. UniverslViewer are evaluated and final decision on server and viewer before Q4 2022.
  • Example CETAF ID: https://w.jacq.org/W0100330

University of Vienna, Herbarium (WU)

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