These publishers granted us permission:

publisher, Medline size, % with 'gene' in abstract Terms of Service allows Text Mining? UC Library License allows Text Mining? Contact First contact Got permission? Transfer, success rate
Elsevier, 1634233 articles (21%)

No: "You may not engage in systematic retrieval of the Site"

Not explicitly prohibited:

Raphael Sidi, VP Product Management ScienceDirect (has left Elsevier) and Jud Dunham, Oct 2009, again in June 2011 Yes, Dec 2011, mining license bound to SciverseApp, developed App for Elsevier Download via Consyn, 93% details
Wiley, 933656 articles (23%)

No: "users may not "download and/or store an entire issue of a Electronic Product or its equivalent;"

Yes: "9. licensee has the right to index, search and data mine the digital copy (...) as long as it does not impede Wiley's servers or service in any way. All such processes are solely for the internal teaching, learning and research purpose of the Licensee"

Duncan Campbell, Associate Director, Journal Digital Licensing, Jan 2012 Yes, May 2012 from site, 78% details
Wolters Kluwer, 595371 articles (13%)

No: "Any reproduction, distribution, performance, display, preparation of derivative works based upon, framing, capturing, harvesting, scraping, or collection of, or creating of hypertext or other links or connections to, any Site Materials or any other proprietary information of WKH, without WKH's advance written consent, is prohibited."

Yes: In addition to the Permitted Use above, solely with respect to Lippinctt Willians & Wilkins Journals ordered by Subscribe hereunder: (...) Authorized Users may use the products to engage in text mining/ data mining activities for legitimate academic research and other educationl purposes

Andrew Richardson, VP Business Development, 04/01/12 Yes, Feb 2012 emails, phone conf, reminder sent, 8% details
Oxford University Press, 191682 articles (28%)

Maybe: The materials on our website may be retrieved and downloaded solely for personal use.

Not explicitly denied:

Richard O'Beirne, Digital and Journals Strategy Manager, Apr 2012 Yes, Apr 2012 (quick!) from Highwire site, 95% details
Informa Healthcare, 191593 articles (16%)

No: "the systematic downloading of content without a written licence, will result in access to the site being blocked"

Yes: Authorized Users may use the material to engage in text mining

Ian Bannerman, Managing Director Journals, Feb 2012 Yes, Refused. Ongoing discussions. 1% details
Nature Publishing Group, 160119 articles (33%)

No: "You may not (...) (b) copy, download, or store any content, files, feeds or data from the Site, whether publically available or not, to make or populate a database or publication of any kind whatsoever"

Explicit: No: the Licensee warrants (...) that it will not (...) (j) make mass, automated or systematic extractions from or hard copy storage of the Licensed Material

David Hoole, Director Brand Marketing and Institutional Relations London, Alf Eaton in Nov 2009, David Hoole in Aug 2011 Yes Feb 2012,Permission via email, license pending, 67% details
American Society for Biochemistry and Molecular Biology, 70679 articles (57%)

No explicitly:

No explicitly:

Andrew Harmon, Science and Publishing Technology Manager, Feb 2012 Yes, Mar 2012, (Highwire) 98% details
American Society for Microbiology, 66429 articles (43%)

No:

Alex Collery, Feb 2012 (Highwire) Yes highwire, 61% details
Karger, 65779 articles (18%)

Yes: "shall be permitted to use information contained in the licensed materials for education, scientific or research purposes"

Sharon Mattern Buttiker, Web Alliance Manager, Feb 2012, retried in Apr 2012 Yes, Oct 2013 from site, 0% details
American Association for Cancer Research, 26545 articles (44%)

Yes: "shall be permitted to extract or use information contained in the licensed materials for education, scientific or research purposes"

Feb 2012, retried in Apr 2012 Yes highwire, 92% details
American Association of Immunologists, 23608 articles (35%)

No license?

:

Claire Sinks, Content Licensing Manager, Apr 2012 Yes, May 2012 highwire, 93% details
Company of Biologists, 19873 articles (41%)

"Prepare derivative works or download, mount or distribute any part of the Licensed Material on any electronic system or network"

:

Jane Pennington, Subscription Sales & Marketing, Apr 2012 Yes, Nov 2012 ?, 91% details
Portland Press, 17407 articles (47%)

 "systematic downloading of content without a written license, will result in access to the site being blocked"

: No license

Caroline Black, Managing Director Mar 2012 Yes, Apr 2012, can crawl Biochem Journal, Biochem Soc Trans "our site is crawlable", 3% details
Royal Society, 16414 articles (10%)

Yes: Licensee may (...) Use Text Mining technologies to derive information from the Licensed Materials.

:

Stuart Taylor, Commercial Director May 2012 Yes May 2012, 6% details
Society for General Microbiology, 14263 articles (65%)

:

Karen Rowlett, Managing Editor IJSEM, Mar 2012 Yes, Apr 2012, four journals, see link, (highwire), send results highwire, 93% details
Cold Spring Harbor Laboratory, 12772 articles (48%)

No: Systematic downloading (by robots or other automatic processes) is prohibited without explicit publisher approval.

:

John Inglis, Executive Director, May 2008 Yes, June 2012 via Highwire, 25% details
American Society for Pharmacology and Experimental Therapeutics, 12310 articles (37%)

No: "The person using an American Society for Pharmacology and Experimental Therapeutics journal may view, reproduce, or store copies of articles comprising the journal provided that the articles are used only for their personal, non-commercial use."

:

Richard Dodenhoff, Apr 2012 Yes, Apr 2012 (UCSC has no sub, but back content 1997- crawlable) highwire, 92% details
Rockefeller University Press, 10753 articles (41%)

No: "The user may not (...) make available a mirror site of the RUP web site, any of its constituent journal web sites"

:

Gregory Malar, Business Development Director, Mar 2012 Yes, Apr 2012 (+highwire account) 97% details
Genetics Society of America, 6785 articles (47%)

: no license

Scott Hawley/Tracey DePellegrin Connelly Aug 2009 Yes, March 2010 highwire, 93% details
Federation of American Societies for Experimental Biology, 5981 articles (49%)

Not explicitely

:

Barbara Walker, Content Licensing and Sales Manager, Apr 2012 Yes, July 2012 highwire, 91% details
Springer, 1 articles (NA)

No: "User may not modify, remove, delete, augment, add to, publish, transmit, participate in the transfer or sale of, create derivative works from, or in any way exploit any of the Content, in whole or in part.

Yes: User may not systematically download any content except for legitimate research purposes

Wim van der Stelt, Executive VP Corp Strategy, Feb 2012 Yes, July 2013 Harddisk and FTP Updates, 0% details
Royal Society of Medicine Press, 1 articles (NA)

Yes: authorized users may "use Text Mining technologies to derive information from the Licensed Materials"

:

Jeremy Theobald, Head of Publishing Feb 2012 Yes, March 2012. (We have no license but they give us access for one year!) Highwire site, 0% details
The British Society of Immunology, 1 articles (NA)

:

Daniel Price, Education & Communication Officer, Feb 2012 Yes, Mar 2012, but download/license via Wiley Mar 2012, 0% details
Society of Molecular Biology and Evolution (Journal: Mol Biol and Evol), 1 articles (NA)

See Oxford University Press

Not explicit:

Ken Wolfe/Cathy Kennedy Feb 2011 Yes, Nov 2011 highwire, 0% details
The Genetics Society (Heredity), 1 articles (NA)

Explicitly yes, but see Nature Publ Group for our separate agreement

:

Yes, July 2009 Oct 2011, 0% details
Future Science Group, 1 articles (NA)

No: "systematic downloading of content without a written license, will result in access to the site being blocked"

:

Elisa Manzotti, Publisher, Mar 2012 Yes, Apr 2012, project progress updates special crawler, 0% details
Am Soc of Plant Biologists (Plant Phys, Plant Cell), 1 articles (NA)

No license?

: No license

Nancy Winchester, Publications Director, Mar 2012 Yes, Mar 2012 (We have no site license. up to 76% is open-access, check: not marked as OA in PMC?) 0% details
American College of Chest Physicians (Chest), 1 articles (NA)

No:

:

Carla Miller, Assistant Editor, Jul 2012 Yes, Aug 2012 highwire?, 0% details

No permission yet from these:

publisher, Medline size, % with 'gene' in abstract Terms of Service allows Text Mining? UC Library License allows Text Mining? Contact First contact Got permission? Transfer, success rate
Sage, 118792 articles (16%)

Yes: "may extract or use information contained in the licensed materials for education, scientific or research purposes"

Feb 2012 No, No reply 5% details
Mary Ann Liebert, 54457 articles (31%)

Yes: Licensed material may be used for purposes of research

Feb 2012 No 0% details
American Physiological Society, 53529 articles (30%)

Yes: "shall be permitted to use information contained in the licensed materials for education, scientific or research purposes"

Mark Goodwin, Editorial Manager, Feb 2012, retried in Apr 2012, retried 4 times No highwire, 0% details
National Academy of Sciences, 46637 articles (42%)

No: "systematic downloading is prohibited"

: No license

Feb 2012 No highwire, 70% details
Bentham Science, 30691 articles (27%)

Yes: Not specified

: No license

Richard E. Morrissy, USA Office No, Mar 2012, again in Apr 2012 1% details
American Medical Association, 23275 articles (8%)

:

:

Feb 2012, retried in Apr 2012 No highwire, 0% details
American Society of Hematology, 17856 articles (36%)

No: "No part of the publication may be reproduced (see exception below), stored in a retrieval system, translated, or transmitted in any form or by any means now or hereafter known, electronic or mechanical, without permission in writing from the publisher, The American Society of Hematology (ASH)."

:

Julie Robertson, Marketing and Advertisigin Coordinator Mar 2012 No, Refused: "Text mining is a service we would not be pursuing at this time." 0% details
Landes Bioscience, 17018 articles (42%)

No: "Nothing contained on the Website will be construed as granting, by implication or otherwise, any right to use, reproduce, modify, transmit, display, publish, sell, create derivative works, publicly perform, or distribute by any means, method, or process whatsoever, now known or hereafter developed, any of the Content on or transmitted through the Website for commercial purposes."

:

Cynthia Conomos Mar 2012 No 5% details
BMJ Group, 11474 articles (8%)

No: Systematic Download is prohibited

No reply yet No, Feb 2012 4% details
Cambridge University Press, 1 articles (NA)

No: you agree NOT to "Engage in systematic copying or downloading of the Materials or transmit any part of the Materials by any means to any unauthorised user"

Yes: No explicit language prohibiting mining or systematic download

M Anderson, Feb 2012, retried in Apr 2012 No highwire, 0% details
American Assoc for the Advancement of Science, 1 articles (NA)

Probably not: Does not address question

Feb 2012 No 0% details
IOS Press, 1 articles (NA)

No: user is not allowed to "systematically make print or electronic copies of the item(s)"

No: No license

Astrid Engelen, Head of Marketing Feb 2012 No Feb 2012 (we have no site license), 0% details
American Soc of Clin Oncology (Journal of Clinical Oncology), 1 articles (NA)

No: using manual or automated software, devices, scripts, robots or other means or processes to access, "scrape," "crawl," or "spider" any Content contained on the Website;"

:

No, Mar 2012 0% details
The Endocrine Society, 1 articles (NA)

No: "Permitted access by authorized users includes searching, downloading, printing and storing of individual articles for scholarly research, educational and personal use. "

:

dbyrnes Feb 2012 No 0% details
The Society for Neuroscience, 1 articles (NA)

No: "Systematic downloading is prohibited."

:

jperry Apr 2012 No 0% details
Others that were contacted in April 2012: Associations of publishers that forwarded our email (thanks!): It is not obivous to find out if crawling is already allowed in the existing license, here is are some public lists of license that I'm using: