3. Elsevier’s New Text and Data Mining Policy
Researchers at academic institutions can text mine
subscribed content on ScienceDirect for noncommercial purposes via the ScienceDirect APIs
Access is granted to faculty, researchers, staff and
students at the subscribing institution
Text mining output can be shared publically
under these conditions
1. May contain "snippets" of up to 200
characters of the original text
2. Should be licensed as CC-BY-NC
3. Should include DOI link to original content
http://www.elsevier.com/tdm
Corporate and other subscribers
• Your Elsevier Account Manager will be
happy to discuss options to meet your
needs
Open access content
• Text and Data mining permission are
determined by the author's choice of user
license. This information is detailed in the
individual articles
3
4. Policy Aligned with the Recent STM
Declaration on TDM
http://www.stm-assoc.org/2013_11_11_Text_and_Data_Mining_Declaration.pdf
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5. Text and Data Mining – What is it?
Data mining: “the computational process of discovering patterns in
large data sets involving methods at the intersection of artificial
intelligence, machine learning, statistics, and database systems”
Text mining: essentially a subset/“input step” to data mining: turning
text into structured data for analysis, via application of natural language
processing (NLP) and analytical methods.
Typical text mining tasks include text categorization, text
clustering, concept/entity extraction, production of granular
taxonomies, sentiment analysis, document summarization, and entity
relation modeling (i.e., learning relations between named entities).
http://en.wikipedia.org/wiki/Data_mining
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6. TDM Examples – Entity Tagging and Linking
http://dx.doi.org/10.1016/j.bbalip.2012.02.009
6
7. TDM Examples – Information Extraction
http://genome.ucsc.edu/
7
8. TDM Examples – Information extraction
http://neuroelectro.org
8
9. TDM Examples – Natural Language Modelling
http://www.elsevier.com/online-tools/pathway-studio/
9
9
10. Text mining is Becoming an Essential Tool
Blue Blain project
• Reconstructing the brain piece by
piece and building a virtual brain
in a supercomputer
• Received €500M (~$685m) of EU
funding
“The success of the Blue Brain project depends on very high volumes of standardized,
high quality experimental data covering all possible levels of brain organization. Data
comes both from the literature (via the project’s automatic information extraction
tools) and from experimental work conducted by the project itself.”
http://bluebrain.epfl.ch/page-58110-en.html
http://bluebrain.epfl.ch/
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12. Supporting TDM at Elsevier
2006
…
• Began to support ad-hoc TDM access requests from customers
• Low but consistently increasing level of interest from early
adopters as computing power increases and tools get better
• First Content Mining policy published
• New APIs and Content Syndication Service rolled out to
2012
provide better technical solutions for TDM content access
• Pilot with ~30 academic customers to better understand needs
and define future policy
2013
• New Text and Data Mining policy for academic customers
announced
2014
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13. TDM Pilot Learnings – Use Cases
Most academic TM requests fall in one or both of these categories:
1. Answering a specific
research question
2. Building a new data
resource for the community
• How long does it take for
concepts in STM literature to
reach general media?
• What is the relationship
between the research and
consulting commitments of
economics and finance
professors?
• What are the characteristics of
subjects in social psychology
experiments?
• An HIV mutation database for
which mutations found in
literature are mapped to the
underlying database sequence
• A database on growth and
alimentation of fishes, and
develop a fish classification to
identify new species for
aquaculture
• A database with the
electrophysiological properties
of diverse neuron types
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14. TDM Pilot Learnings – Researcher Challenges
Technical
• Obtaining necessary infrastructure
• Having to deal with different formats from
content providers
• Sourcing and understanding TDM technology
Functional
• Fine-tuning pipeline, curating output,
representing output meaningfully
Logistical/Legal
• Gaining access to the needed content
• Gaining permission to mine the content
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15. TDM Pilot Learnings – Library Challenges
Expertise
• Understanding specific TDM-based projects well
enough to assess implications & offer advice to
patrons
Legal
• Understanding and tracking what is allowed for
what resources
• Negotiating permissions with multiple providers
• Ensuring academic freedom is protected
Financial
• Concerns about any additional costs
• Understanding how TDM affects usage figures
for the library
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16. TDM Pilot – Conclusions
1. Elsevier can offer enhanced value to
ScienceDirect customers by including basic text
and data mining access rights in subscription
agreements
2. Self-service access to content for TDM via our
APIs meets the needs of most researchers in
academia
3. There is demand for services beyond basic
content access that make text mining easier
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17. TDM Access: What do Institutions
Need to do?
• TDM access clause will be part of standard
ScienceDirect subscription agreement for new
academic customers and upon renewal
• For existing agreements, an add-on contract
amendment is available – just contact your Elsevier
Account Manager
• After signing institutional agreement/amendment,
access to our API key registration page for your
researchers will be enabled for your institution’s IP
address range
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18. TDM Access: What do Researchers
Need to do?
1. Register at http://developers.elsevier.com
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19. TDM Access: What do Researchers
Need to do?
2. Accept a simple click-through agreement
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20. TDM Access: What do Researchers
Need to do?
3. Obtain an Elsevier API Key
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21. TDM Access: What do Researchers
Need to do?
4. Use API Key to retrieve full text of journal articles
and book chapters via the Elsevier API
• Elsevier XML and plain-text formats supported
• We are looking into supporting specialized textmining friendly XML formats
5. Process retrieved full-text through text mining
tools/workflow of choice
Documentation available on developer portal
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22. Why an API? Can’t we just crawl
ScienceDirect.com?
• We are providing separate channels for machine-tomachine and human access to content
• This helps us to maintain site performance, availability
and reliability for everyone
• Other major web information sources have similar
policies
• Wikipedia:
http://en.wikipedia.org/wiki/Wikipedia:Database_download
• Twitter: https://twitter.com/tos
• PubMed Central:
http://www.ncbi.nlm.nih.gov/pmc/about/copyright/
• People who text-mine prefer APIs!!
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25. Supporting Cross-publisher TDM
Prospect is a new service from CrossRef providing two components to
address the issue of text and data mining scholarly literature across multiple
publishers:
• The “Prospect Common API” (PCAPI) can be used to access the full text of content
identified by CrossRef DOIs across publisher sites and regardless of their business
model.
• The “Prospect License Registry” (PLR) can (optionally) be used by researchers and
publishers as an efficient mechanism to provide “click-through” agreement of proprietary
TDM licenses.
• Both components are free to use by researchers and the public
https://prospect.crossref.org/
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27. Elsevier and Prospect
Elsevier is the first publisher to fully integrate with the
Prospect beta system:
• Researchers may read and agree to the Elsevier TDM clickthrough agreement via the Prospect License Registry
• Researchers may use a Prospect token to access Elsevier
content through the Prospect Common API rather than
using the Elsevier-specific API Key and Elsevier API
• Content is available in the same formats as the Elsevier API
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28. Outlook: Beyond Basic Access
Text Mining as a Service
• Pilot with NaCTeM to
integrate their tools with
Elsevier content
• Hosted in the cloud
• Avoids the need for
researchers to build and
maintain TDM infrastructure
• Ability to define and execute
TDM workflows in a graphical
environment
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29. Takeaway Points
• Researchers at academic institutions can now textmine subscribed Elsevier content for noncommercial purposes at no additional cost
• Contact your Elsevier Account Manager if you are
interested
• Elsevier is collaborating with customers and industry
partners to make text mining easier
• More info at: http://www.elsevier.com/tdm
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The requirement for licensing TDM output as CC-BY-NC only really applies to TDM Output insofar as it includes copyrightable material derived from the Elsevier content. For instance, we don’t require that any papers written about the TDM findings are published under CC-BY-NC.
Elsevier is one of 16 publishers signing the declaration. Note that the Elsevier policy is _not_ limited only to the EU.
TDM is a very large domain that encompasses many concepts. What follows are three examples of text mining-based operations on scholarly literature.
Content tagging is not new – we (and librarians) have done that for years – manually. Thesauri are used to classify and index publications. Text mining technologies, however, allow us to that in automated ways, covering vast corpuses very quickly and increasingly accurately.
Text mining is no longer purely the subject of research itself, nor just an experimental tool used by tech-savvy researchers. It is a core component of an increasing number of research projects and for many of those projects, text mining is critical for their success. An example of a project that uses text- and data mining extensively is the Blue Brain project, one of the flagship research projects in the European union and recipient of a 500 million euro (>650M US dollars) grant.
Here is a typical text mining workflow, courtesy of NaCTeM at University of Manchester:A corpus of source documents is collected and preparedA part-of-speech tagger runs over the documents, breaking down the sentences by grammatical syntaxTerms are normalized: plural vs. singular, alternative spellings, etc.Acronyms are identifiedA value is calculated that expresses the accuracy of a specific term’s automatic recognitionExtracted terms are consolidated into a databaseThe source documents are annotated with the extracted, normalized terms, and the terms are analyzed
Elsevier has supported requests from researchers for text mining access on an ad-hoc basis for several years. Demand has gradually increased as computing power increased and more tools became available. In 2012, we made investments to improve our technological support for these needs, and in 2013, ran a formal pilot to better understand researcher needs and help us design an appropriate technical and legal policy to meet those needs.
One of the key learnings from the pilot was that academic needs for TDM typically fall into one of both of two categories.
As solution for TDM is designed to address several of the key challenges researchers currently have: specifically, to make it easier to gain permission to mine and to access content in a simple and effective way suitable for text mining workflows.
Librarians also face challenges in supporting TDM needs of their researchers. Our new policy is designed to allow librarians to fulfill those needs quickly and simply with no additional cost.
Our experiences have led us to two conclusions: we need to a. support basic access for do-it-yourself text mining, and b. there is an opportunity for making text mining easier
Probably good to mention that you’ll talk about Prospect later.
Probably good to mention that you’ll talk about Prospect later.
Probably good to mention that you’ll talk about Prospect later.
Probably good to mention that you’ll talk about Prospect later.
We also recognize that researchers typically want to mine content across multiple publishers, so we are leading participants in a new industry initiative designed to make that easier.