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Nigel Robinson - ZooBank and Zoological Record: a partnership for success
The document discusses the partnership between Zoological Record (ZR) and ZooBank to provide taxonomic and nomenclatural information. ZR is the oldest continuing life science reference database, indexing over 72,000 items annually from 5000 journals. It captures metadata on new species names and has an archive of over 1.7 million articles. Through the Index to Organism Names project, ZR provides links from species names to relevant information. The partnership with ZooBank will provide stability, technology, and open access to taxonomic data and literature links for the scientific community.
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Nigel Robinson - ZooBank and Zoological Record: a partnership for success
- 1. Zoological RecordTM & ZooBank: apartnership for success Nigel Robinson Director, Operations & Development Thomson Zoological Limited
- 2. Association with thecommunity • 1864 – Scientists associated with British Museum & Zoological Society • 1880-1980 – Zoological Society support • 1980-2003 – Zoological Society/BIOSIS partnership • 2003 – BIOSIS • 2004 – Thomson Scientific • Zoological Record & data capture • Index to Organism Names project
- 3. Zoological Record • Oldestcontinuing life science reference database • Comprehensive coverage • Unparalleled breadth and depth of coverage of biodiversity, zoology and animal biology • Authoritative record of taxonomy & nomenclature • New names with metadata • Taxonomic & nomenclatural acts • High archival value
- 4. Zoological Record content •32 staff in York • 5000 journals, plus conference proceedings, books, monographs from 100 countries – bring together disparate sources • 72,000 items per year • Gather 20,000 new names per year • Metadata currently gathered • Name • Authorship • Reference • Type locality (country level) • Type horizon • Type host • Page in journal where description appears • 1.7 million article archive to 1978…….and growing • Monthly updates
- 5. Zoological Record andThomson • Durable – ZR is still here 150 years on • Most up to date • Items indexed in 2-11 days of receipt • Most complete • Involved in the taxonomic / biodiversity community • Financially stable future • Backed by the resources of the Thomson Corporation • Archive digitization • BiologyBrowser • Index to Organism Names
- 6. The ZR/ZooBank partnership •Partnership • Stability & longevity • Technology • Data and links – open access • Agreements with publishers and libraries • Obtaining material to index • Providing links to full text of the article/description • Ongoing data capture & quality checking • Existing names back file • A free, open access service for the community
- 7. Index to OrganismNames (ION) • Under redevelopment for imminent release • >1.5 million names from ZR 1970-present • Plus names from BIOSIS Previews® & Biological Abstracts® • Links to Web information, Zoological Record (Biology, Taxonomic history, Full text article, Power of the Web of Knowledge) • Alerts to new names for specific groups • Purpose and uses • Homonym checking & use of name in the published literature • Identify the taxonomic group to which an organism belongs • Verify that newly published animal names have been correctly reported in Zoological Record, as recommended by the Code, and submit omissions • Obtain literature references about a name • View latest research carried out on a name through the recent articles list • Access full text and gain access to the full literature record of a given name www.organismnames.com
- 8. Index to OrganismNames Enter a basic or advanced search Browse and search for names using the taxonomic hierarchy
- 9. Index to organismNames - Details View results list and expand to see details Links to indexing and full articles Recent articles and web sites
- 10. Zoological Record Indexing Abstract Indexing& additional nomenclatural acts Links to full text
- 11. Index to OrganismNames - submission Users can submit publications or names for inclusion in ZR
- 12.
Editor's Notes
- #2 Thank you for the opportunity to talk about the very exciting partnership between Zoological Record and ICZN in the context of the ZooBank project. I am based in York, UK at Thomson Zoological where the Zoological Record is produced and I head the York office which forms part of the global Thomson Company, within the Academic & Government sector of Thomson Scientific, focusing on providing information for the scientific research community.
- #3 Since its origin in 1864, ZR has had a close association with the taxonomic community, particularly with the Zoological Society of London. ZR was founded in 1864 by a group of scientists associated with the British Museum. It continued, supported by Society until 1980 when a partner was sought and BIOSIS took over production activities. In 2004, BIOSIS realised that with limited resources we could not achieve our aims and put our ideas into practice without further partnerships, so in January 2004, BIOSIS (including ZR) was acquired by the Thomson Corporation, and the new ownership is now starting to pay dividends – more of that in a moment. Over that 150 years or so, there have been difficult times, but ZR is still here and still has the same purpose it had in 1864 - to serve the community and disseminate taxonomic, biodiversity and zoological information for the benefit of scientific research. In the short time we have available, I will bring you up to date on where Zoological Record stands today – I assume most people are familiar with it to some degree - and go on to discuss our new free Index to Organism Names service to demonstrate our commitment as Thomson to this initiative. I will also discuss how the partnership between ZR and ICZN might work from the ZR perspective.
- #4 As most of you will be aware, Zoological Record is the oldest continuing life science reference database and has unparalleled coverage of published taxonomic changes, new taxa and biodiversity related information. New names are recorded individually – with associated metadata – whether fossil or extant. That coverage continues and remains core to our business; it is very much a Thomson policy to reflect those user requirements in our services. Market research shows an incredibly high level of user satisfaction in all areas other than depth of electronic online backfile. This is the first area where Thomson resources have been able to provide us with the means to digitize ZR from 1864, so from mid 2006 you will be able to search all of ZR and all the new names previously only available in the printed ZR back to 1864 in a single search and link through to original articles where available. This is a sign of commitment to ZR from Thomson and something which could not have been done as effectively under BIOSIS. This is only possible with the resources of a global company supporting the initiative. With the 150 year backfile, ZR has high archival value – no one else has the wealth of names – we have seen a myriad of web based systems and none have the coverage of ZR.
- #5 So - How do we compile ZR? Over 5000 journals plus, books, monographs, meetings/conferences etc. are monitored each year to extract and index relevant articles. Currently we include over 72,000 items per year from journals published in over 1000 countries. As part of our indexing we gather ~20,000 new names per year, 4000 new synonyms and 4500 new combinations. Each name has appropriate metadata relating to the taxonomy or nomenclatural act. In electronic form we have 1.7 million items available online and which are added to monthly. This will reach ~3 million with the release of the additional back years in 2006
- #6 So, we have been through difficult times. ZR is still here – will others be here in a few years time? Many are grant funded and need to commercialise themselves to survive. ZR is already in that sitiuation and is self supporting and is backed by a global organization. As you may be aware, there was a period in the 80s where ZR was out of date and was heading for financial difficulties, but under BIOSIS that stabilized out. We are now up to date and items are generally indexed within 2-11 days of being received at ZR, and we are backed by a committed, global company. Completeness . we are well over 90% complete and probably over 95%. With the resources of Thomson that can only improve and with involvement in the registry it could be 100%. We now have improved publisher relations and receive ~80% of materials direct from the publishers. Accuracy: all new names are gathered and double checked manually by graduate zoologists. In addition we have machine files to check the names a third time and it is impossible to now enter a name into our system without it going through and passing these checks, so accuracy is extremely high Yes, we are a commercial company, but I don’t necessarily think that is something to be afraid of or back away from. It brings stability and commitment to the table with real ongoing survival. The days are gone when we could sit back and wait for people to buy ZR – and with complex systems and 32 staff required to produce ZR, we need the revenue to finance its production. We have the backing of a highly successful company who is committed to supporting ZR and derived services, but is also willing to provide free services. Our free web services BiologyBrowser and ION which Thomson are funding the development are testament to the company’s commitment, and we have continued in our support of the taxonomic community through involvement with GBIF, Species 2000 (for whom we host the website and provide technical programming resources to maintain it; we also run the wrappers and servers for the annual and dynamic checklists – commit 30% of a person) So with that commitment in mind, I’ll explain how the relationship between ZR and ICZN might work……
- #7 There are many things we can bring to the table. We see this very much as a partnership and that the registry/ZooBank should be run and administered by ICZN for the community. However, given the data we already collect for ZR, the way we collect them, the resources and commitment of the Thomson organisation and the services we are running, we are in an ideal position to help move the project along and assist, particularly with the names included in published literature, which would be indexed in ZR anyway. Partnership : agree that ICZN is the body to spearhead this and we would not seek to take that away. Would rather work in partnership with ICZN, but it seem there are a number of items which are instantly resolved at no cost if use is made of existing or slightly modified processes already in place in ZR Technology : Thomson and ZR in particular have existing technical expertise which is already being used in open access community resources like Sp2000 (websites, grant money), ION, BiologyBrowser, open access linkages Stability & longevity: we understand sustainability is paramount. I would suggest this is achieved more easily by partnering with a successful company rather than grant funded bodies. Thomson have shown commitment, and would hope we could fashion an agreement such that the commitment was ongoing. Links: ZR already links to many journals through publisher agreements which would be necessary and are already talking to museums and other bodies with a view to implementing links to their full text services which would include more than just open access journals. Through our Web of Knowledge platform, we can easily implement links to these sources. There are other opportunities as we digitize back to 1864 to link to digital archives as they are created. Data capture, quality checking, correcting and archiving: ZR has over 140 years experience of doing this efficiently and a skilled, ready trained workforce. ZR has established high quality data capture which could be easily adapted to gather required data and check conformity to Code, providing standardisation and completeness. We have discussed ways we can adapt our indexing system to capture additional data required by ZooBank to check availability criteria. We believe that for published literature this approach would be the most complete, accurate and reliable way to build ZooBank data at no cost to ICZN. We have doubts that the 20,000 new names each year could be captured by author entry or by other third parties. Once captured, that data would need to be checked and verified. This process is already in place and ZR is willing to share the results with ICZN – in fact the data is already there in ION. By exploiting what already exists in ZR systems, many potential problems simply disappear. For Existing names, ZR is the most comprehensive source of original new name description references. Others are incomplete, lack fossil taxa, and all are looking to use ZR to fill gaps. It is likely that we will have links to Barcoding of Life project, Species 2000/ITIS, GBIF specimen data, all of whom want to fill their gaps with ZR data. We already have commitment from Thomson senior management in support of ZooBank and ION going forward. No one else has 140 years of indexed searchable taxonomy. So with that in mind, I would like to finish by discussing the new ION service which will be available soon and incorporates many of the features proposed for ZooBank.
- #8 Free service, open to all Provides basic taxonomic information on all names indexed in Zoological Record, plus names from the non animal literature, plus: Links to ZR indexing, references in ZR and full text articles subject to appropriate subscriptions Links to valuable verifies and indexed Web resources provided by ZR staff Recent article lists Full bibliographic reference for original descriptions indexed in ZR New names alerts by RSS feed Ability to submit articles and names for indexing on ZR Purpose and uses: Homonym checking not only within zoology, but also from botany and micro-organisms Check if name has been used in the published literature Identify the taxonomic group to which an organism belongs Verify that newly published animal names have been correctly reported in Zoological Record , as recommended by the International Code of Zoological Nomenclature, and submit articles to have names included Keep up to date with newly published names in your organism group Track changes in the actual usage of names (and their variant spellings) in the literature Check homonyms - avoid homonym creation for new names and identify existing homonyms within and between phyla or kingdoms Obtain literature references about a name View latest research carried out on a name through the recent articles list Access full text and gain access to the full literature record of a given name Launch will be announced on TAXACOM and other email listservs
- #9 The names can be searched in basic or advanced mode, or via a browsable hierarchy
- #11 Linking to the Zoological Record indexing provides access to the additional taxonomy and nomenclatural acts indexed for the item and gives access to the abstract and full text for many articles. It opens up the full power of the Web of Knowledge for analysis of the articles retrieved.
- #12 The publication containing the reference can be supplied as A citation for ZR to locate A PDF file (emailed as an attachment) via the submission form A web site reference Hard copy
- #13 RSS feeds of names recorded as new are supplied as monthly alerts. Users can select the group(s) they want to monitor. There is no limit to the number of groups which can be monitored
- #14 So we very much look forward to working with the ICZN on this initiative to create a prototype ZooBank site for comment over the coming months.