BHL has deployed a new taxonomic name finding tool to improve the speed and accuracy of identifying names throughout its 58+ million pages.

BHL is now using Global Names Architecture’s (GNA) gnfinder tool to locate taxonomic names in the BHL corpus. Prior to this deployment, BHL’s name finding services were based on an index of scientific names created by GNA developers six years ago by parsing every page in BHL one by one. This took 45 days to accomplish, and the cost of repeating this process made updating or improving the index infeasible.

The gnfinder tool uses fast, scalable programming languages to significantly reduce computational time. Using Open Source applications in Go and Scala, the tool detects candidate scientific names and compares them to millions of scientific name-strings aggregated by GNA for verification. The new process decreases the time needed for name detection and name verification from 35 days to 5 hours and from 7 days to 12 hours, respectively. As a result, the entire BHL corpus can now be indexed in less than a day, compared to the 45 days needed for the previous index. Additionally, by significantly reducing computational time, implementing iterative improvements to the index is now achievable.

The accuracy of the names identified has also been improved with this deployment. By eliminating questionable results and false positives from the previous index, gnfinder produces a more accurate index of names in BHL. More than 34 million unique names — representing more than 239 million total instances of taxonomic name strings — were identified across the BHL corpus as of 21 July 2020. Of these, approximately 11.7 million are “Verified Names”, meaning they are unique names that have been resolved against a name authority (NameBank, Catalogue of Life, etc).

The gnfinder tool was developed by Dmitry Mozzherin and Alexander Myltsev as part of GNA project work at the University of Illinois at Urbana-Champaign. Mozzherin shared more about the process of developing this tool at the Biodiversity Next conference in Leiden, The Netherlands in 2019. Learn more in the presentation slides.

You can learn more about how the BHL implementation of the gnfinder tool works in our FAQ.

We would like to thank our colleagues at Global Names Architecture — especially Dmitry Mozzherin, Alexander Myltsev, and David Patterson — for their work to develop these tools. Thanks also to Joel Richard (BHL Technical Coordinator and Head of Web Services and IT at Smithsonian Libraries) and Mike Lichtenberg (BHL Lead Developer) for their work to deploy gnfinder on the BHL website.

If you have questions about gnfinder or would like to provide feedback or suggestions, please contact Global Names Architecture via the Global Names BHL project on GitHub.

Global Names development on BHL indexing is supported by National Science Foundation grants #1356347 and #1645959 as well as the Species File Group at the University of Illinois.

The BHL API will be updated on 25 July 2016 to support changes to the BHL site. These changes will accommodate identifying additional Contributors for Items and Parts of items.

First are changes to the API that may affect your existing processes.

The Contributor and ContributorID elements in the result sets of API methods that return “Part” information will move. ContributorID will be included as a PartIdentifier in the Identifiers list. Contributor will be included in a new Contributors list.

These changes are being made to accommodate more than one contributor per part.  For example, if one institution researches/compiles the data and a second institution facilitates the inclusion of that data in BHL, both institutions may be listed as a contributor.  Initially, no more than two contributors per part will be allowed, but by adopting these changes to API responses we allow for additional (unlimited, actually) contributors in the future.

Here is an example that shows how the API responses are changing.  The examples shown here are an output of the GetPartMetadata method, and have been abbreviated for clarity.

Original API Results – highlighted elements are being moved:

<Response>
 <Status>okStatus>
 <Result>
 <PartUrl>
        http://www.biodiversitylibrary.org/part/1
 PartUrl>
 <PartID>1PartID>
 <ItemID>22498ItemID>
 <StartPageID>3190776StartPageID>
 <SequenceOrder>1SequenceOrder>
 <Contributor>BioStorContributor>
 <ContributorID>4443ContributorID>
 <GenreName>ArticleGenreName>
 <Title>
      Notes on certain species of Tetragnatha 
      (Araneae, Argiopidae) in Central America 
      and Mexico
 Title>
 <ContainerTitle>BrevioraContainerTitle>
 <Volume>67Volume>
 <Date>1957Date>
 <PageRange>1--4PageRange>
 <StartPageNumber>1StartPageNumber>
 <EndPageNumber>4EndPageNumber>
 <Authors> [...] Authors>
 <Subjects />
 <Identifiers>
 <PartIdentifier>
 <IdentifierName>ISSNIdentifierName>
 <IdentifierValue>0006-9698IdentifierValue>
 PartIdentifier>
 Identifiers>
 <Pages> [...] Pages>
 <RelatedParts />
 Result>
Response>

Updated API Results – Highlighted elements are the new locations of the moved data:

<Response>
 <Status>okStatus>
 <Result>
 <PartUrl>
        http://www.biodiversitylibrary.org/part/969
 PartUrl>
 <PartID>1PartID>
 <ItemID>22498ItemID>
 <StartPageID>3190776StartPageID>
 <SequenceOrder>1SequenceOrder>
 <GenreName>ArticleGenreName>
 <Title>
        Notes on certain species of Tetragnatha
        (Araneae, Argiopidae) in Central America
        and Mexico
 Title>
 <ContainerTitle>BrevioraContainerTitle>
 <Volume>67Volume>
 <Date>1957Date>
 <PageRange>1--4PageRange>
 <StartPageNumber>1StartPageNumber>
 <EndPageNumber>4EndPageNumber>
 <Authors> [...] Authors>

 <Contributors>
 <Contributor>
 <ContributorName>BioStorContributorName>
 Contributor>
 Contributors>
 <Subjects />
 <Identifiers>
 <PartIdentifier>
 <IdentifierName>BioStorIdentifierName>
 <IdentifierValue>4443IdentifierValue>
 PartIdentifier>
 <PartIdentifier>
 <IdentifierName>ISSNIdentifierName>
 <IdentifierValue>0006-9698IdentifierValue>
 PartIdentifier>
 Identifiers>
 <Pages> [...] Pages>

 <RelatedParts />
 Result>
Response>

Additionally, there will be two additions to the Item metadata.

The new data elements are: RightsHolder and ScanningInstitution.
These will optionally be displayed if there is data for the relevant organizations.

<Response>
 <Status>okStatus>
 <Result>
 <ItemID>59382ItemID>
 <PrimaryTitleID>20770PrimaryTitleID>
 <ThumbnailPageID>17605914ThumbnailPageID>
 <Source>Internet ArchiveSource>
 <SourceIdentifier>bulletin5160hatcSourceIdentifier>
 <Volume>v.51-60 1898-99Volume>
 <Year/>
 <Contributor>
      UMass Amherst Libraries (archive.org)
 Contributor>
 <RightsHolder>
 Biodiversity Heritage Library
 RightsHolder>
 <ScanningInstitution>
 Smithsonian Institution Libraries
 ScanningInstitution>
 <Sponsor>UMass Amherst LibrariesSponsor>
    [...]
 Result>
Response>

Detailed documentation for the BHL APIs is available at http://www.biodiversitylibrary.org/api2/docs/docs.html.  It will be updated to reflect these changes after they are moved into production on 25 July 2016.

Go to http://www.biodiversitylibrary.org/getapikey.aspx to get an API key for BHL.

Information about other BHL developer tools can be found at http://biodivlib.wikispaces.com/Developer+Tools+and+API.

If you have questions, please feel free to submit feedback via this form.

This week we feature another of our faithful BHL users, Dr. Toby Musgrave, whose work in horticulture has benefited greatly by his discovery of BHL. We asked him a few questions about how BHL has impacted his work, and we present them to you here in a traditional question and answer style.

Q: What is your title, institutional affiliation, and area of interest?

A: Independent Scholar, unsalaried Research Associate at Royal Botanic Garden, Edinburgh, UK; and unsalaried Group Member of Interdisciplinary Evolutionary Studies (IES) within the Institute of Philosophy and the History of Ideas at Aarhus University, Denmark.

Q: How long have you been in your field of study?

A: My PhD was in garden history and I have been a freelance/independent scholar since 1994.

Q: When did you first discover BHL?

A: 2009

Q: What is your opinion of BHL and how has it impacted your research?

A: A hugely useful resource that has made my research less time consuming and less expensive/

Q: How often do you use BHL?

A: At least monthly

Q: How do you usually use BHL (read the titles online/download whole PDFs/Select Pages to Download/etc.)

A: Download whole PDFs

Q: What are your favorite features/services on BHL?

A: The range of publications available and the ability to request titles to be scanned.

Q: If you could change one thing about BHL, what would it be, or what developmental aspect would you like the BHL team to focus on next?

A:

• To have scanned and available every title listed by Blanch Henrey in her British Botanical and Horticultural Literature before 1800 (Oxford University Press, 1975)
• Continue digitizing horticultural periodicals from the 19th century

Q: If you had to choose one title/item in BHL that has most impacted your research, or one item that you prefer above any other in BHL, what would it be and why?

A: Last year I threw down the gauntlet to [BHL staff] and asked if there was any possibility of BHL arranging to have made available the entire run (1841-1955) of the UK periodical The Gardeners’ Chronicle. I asked because there is nowhere in my country of residence (Denmark) that holds it, requiring that I make time consuming and expensive research trips to London or Cambridge in the UK should I wish to examine the periodical. I was amazed and delighted that BHL has achieved what I asked. This contribution to the BHL catalogue has been a real boon to my research, with the bonus of being able to keyword search the PDFs of annual volumes that often run to in excess of 800 pages of tiny print. Thank you!

And thank you, Dr. Musgrave, for your faithful use of BHL and for taking the time to communicate with us to tell us how we could improve BHL for you! We will get to work on Blanch Henrey’s list of botanical and horticultural works.

For more information about Dr. Musgrave, visit his website at www.TobyMusgrave.com.

And if you have suggestions on how to improve BHL, or if you would like to be featured in our BHL users series on this blog, let us know via our feedback form, send a tweet to @BioDivLibrary, or post on our Facebook wall. We look forward to hearing from our users and continuing to develop BHL in the directions most beneficial to them.

Continuing with our new series on our users and their interaction with BHL, this week we feature Dr. Charlotte Sleigh, Senior Lecturer in History of Science, University of Kent (UK), which we present in a typical question and answer interview style. So without further ado, meet Dr. Sleigh, and read what she has to say about how BHL has impacted her work, and what she would like to see from BHL in the future.

Q: What is your particular area of interest/study?

A: Historian of science with a special interest in natural history.

Q: How long have you been in your field of study?

A: 12 years

Q: When did you first discover BHL?

A: About a year ago.

Q: What is your opinion of BHL and how has it impacted your research?

A: BHL makes many old, rare or hard-to-access science and natural history texts available at the click of a mouse. In the past, if I was not sure whether or not a book was relevant to my research, I would have to make a trip to London or other major archive, and seek it out, perhaps spending a whole day only to find it was not relevant. Now I can check quickly and easily online, flicking through texts. Nine times out of ten I can get what I want from relevant texts by reading online; sometimes I supplement this by looking at another copy or edition in the flesh. Even in this latter case, however, reading online first (and re-checking afterwards) is an integral part of the research. My research has been enhanced in that I am quickly able to cross-reference the work of many scientists and naturalists against one another.

Q: How often do you use BHL?

A: It depends on whether I am in a research-intensive phase; if so, maybe average 2-4 texts per week.

Q: How do you usually use BHL (downloading whole PDFs/reading online/selecting pages to download/etc.)?

A: Read online. I also go to the text-only version at archive.org to search the text for key words, then go back to read the relevant pages at BHL online.

Q: What are your favorite features/services on BHL?

A: As above, the ability to search for key words, though this is a bit of a clunky, multi-stage process.

Q: If you could change one thing about BHL, what would it be, or what developmental aspect would you like the BHL team to focus on next?

A:

• Easier access to text-only version.
• My browser (Explorer) sometimes struggles with magnification and gets stuck on a super-enlarged corner of the page.
• Search facility can be a bit hit and miss.
• Otherwise – I would just like to see more titles continuing to be added!

Thank you, Dr. Sleigh, for taking the time to tell us about your experience with BHL. At BHL, we particularly appreciate honest feedback about how we can best focus our resources for further development. The best way to determine this is, of course, to ask those who use our services. So, if you have suggestions on how to improve BHL, or if you would like to be featured in our BHL User series on this blog, let us know via our feedback form, send a tweet to @BioDivLibrary, or post on our Facebook wall. We look forward to hearing from our user community, and also to future opportunities to feature our users.