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Announcements to NLM Data Licensees: Year 2013

(12/03/13) DIRLINE® Ends Its 30 Year Run

(11/13/13) Renew License to Continue Access to 2014 Data (for current MEDLINE®/PubMed®, Catfile, CatfilePlus, Serfile, CCRIS, ChemIDplus Subset, DIRLINE®, GENE-TOX, HSDB® Subset, and TOXLINE® Subset Licensees)

(10/17/13) MEDLINE/PubMed Sample Records using 2014 DTD and Annual Renewal Reminder

(08/13/13) 2014 DTD and XML Changes; Forthcoming 2014 Baseline and Update Files; Schedule Changes; Continuing to Lease NLM Data in 2014

(07/03/13) Computer Retrieval of Information on Scientific Projects (CRISP) Sub-file No Longer Available via NLM Data License

(06/19/13) New NLMMedlineCitationSet DTD dated May 1, 2013 Now in Effect

(06/07/13) Scheduled Maintenance at NLM June 8, 2013 from 8 am to 5 pm ET

(05/15/13) Changes to NLMMedlineCitationSet DTD AND MEDLINE/PubMed XML

(04/11/13) NLM now using RDA: Resource Description and Access for all original cataloging of modern material

(03/08/13) MeSH Unique Identifiers Length Expanding to Ten Characters

(01/07/13) Catfile, CatfilePlus and Serfile MARC 2013 Baseline Files Now Available

(12/17/12) MEDLINE/PubMed Data Changes and More MeSH 2013 Modifications

(12/11/12) 2013 MEDLINE/PubMed Baseline Data; CatfilePlus and Serfile XML Baseline Files

2012 Announcements



DIRLINE® Ends Its 30 Year Run

December 3, 2013

NLM is no longer adding, updating or maintaining records in DIRLINE. Please see the NLM Technical Bulletin article titled “DIRLINE Ends Its 30 Year Run” at http://www.nlm.nih.gov/pubs/techbull/nd13/brief/nd13_dirline_ceased.html for details. Also, on November 28, 2013, NLM posted the final DIRLINE XML data file for licensees on our public FTP server.


Renew License to Continue Access to 2014 Data (for current MEDLINE®/PubMed®, Catfile, CatfilePlus, Serfile, CCRIS, ChemIDplus Subset, DIRLINE®, GENE-TOX, HSDB® Subset, and TOXLINE® Subset Licensees)

November 13, 2013

Licensees who entered into the current License Agreement for NLM Data on or before August 31, 2013 need to renew their license no later than December 11, 2013 to be retained as licensees and to have access to the 2014 data files. An e-mail announcing access to the renewal instructions was sent to those who need to renew. An online system is used to renew or to cancel your existing license. The system will be in operation through 5:00pm EST Wednesday December 11, 2013. If you do not renew by then you will need to submit a new license request to again license the NLM data. If you entered into the current License Agreement for NLM Data on September 1, 2013 or later you do not need to renew for 2014. In this case, you were not sent the e-mail and can ignore the instructions below; your license remains in effect, and access to the 2014 data files will continue without interruption.

RENEWAL INSTRUCTIONS FOR LICENSEES
  1. Go to the renewal system Web page (http://wwwcf.nlm.nih.gov/nlm_licensee/renewal/index.cfm) no later than 5:00pm EST December 11.
  2. Sign into the renewal system. Enter your license code and the licensee’s first and last names exactly as shown in the individual e-mail sent to each licensee on November 13, 2013. Sign in will not work if the secondary representative’s name is entered.
  3. Follow the prompts to renew or cancel your license.

If you elect to renew, you will be asked to re-accept the terms of the license agreement and to review your license profile before electing to renew with or without changes to your profile information. Changes to e-mail address, selecting additional data to lease, or changing an IP address used to get to the data files will take effect immediately. An e-mail confirmation of the renewal will be sent to the license representatives.

If you elect to cancel your license, you will no longer have access to licensed data files on December 17, 2013 and your license will be cancelled on that date. An e-mail confirmation of the cancellation will be sent to the license representatives. See Section 13 E of the License (http://www.nlm.nih.gov/databases/license/license.pdf) for required actions upon termination of the license. Section 6 is also pertinent if you have redistributed data received under this license, or data derived from the NLM-supplied data.

On December 17, 2013 NLM will cancel licenses of those who have not renewed or cancelled on their own by December 11, 2013. There will be no grace period after December 11 as the renewal system will no longer be operational. Licensees who intended to renew but did not do so on time will need to initiate a new license request (http://www.nlm.nih.gov/databases/license/license.html).


MEDLINE/PubMed Sample Records using 2014 DTD and Annual Renewal Reminder

October 17, 2013

  1. MEDLINE/PubMed Sample Records using 2014 DTD
    A small file containing 161 representative records processed using the 2014 NLMMedlineCitationSet DTD is available at http://www.nlm.nih.gov/databases/dtd/medsamp2014.xml. A link to the 2014 DTD and a summary of XML changes for 2014 are in item 1 of the August 13, 2013 announcement at http://www.nlm.nih.gov/bsd/licensee/announce/2013.html#d08_13.
  2. Annual Renewal Reminder
    If you entered into the current License Agreement for NLM Data on or before August 31, 2013 you will receive another e-mail in early November announcing availability of the renewal period for continuation as an NLM data licensee for 2014 data. Please refer to item 5 of the August 13, 2013 announcement at http://www.nlm.nih.gov/bsd/licensee/announce/2013.html#2014LEASE. You do not have to renew for 2014 if you became a licensee September 1, 2013 or later and NLM will not send you the renewal e-mail.

2014 DTD and XML Changes; Forthcoming 2014 Baseline and Update Files; Schedule Changes; Continuing to Lease NLM Data in 2014

August 13, 2013

Topics covered:

  1. DTD and XML Changes for the NLM 2014 Production Year
  2. MEDLINE/PubMed Data Changes for the NLM 2014 Production Year
  3. Forthcoming 2014 Baseline and Update Files
  4. Schedule Changes for Daily MEDLINE/PubMed Update Distributions in November 2013
  5. Continuing to Lease NLM Data in 2014
  6. Information Page for Licensees
  7. License Code Reminder

  1. DTD AND XML CHANGES FOR THE NLM 2014 PRODUCTION YEAR

    There are no changes expected for 2014 to the DTDs used for CCRIS, ChemID Subset, DIRLINE®, Gene-Tox, HSDB®, and TOXLINE® Subset data. There are changes to the DTDs used for MEDLINE/PubMed, CatfilePlus in XML, and Serfile in XML for the 2014 production year. The May 1, 2013 version of the NLMMedlineCitationSet DTD and the January 1, 2013 version of the NLMCatalogRecordSet DTD currently in effect will be replaced by DTDs dated January 1, 2014. The new DTDs will be used for creating the 2014 versions of the baseline MEDLINE/PubMed, CatfilePlus in XML, and Serfile in XML data and their subsequent updates during the 2014 production year. The forthcoming 2014 DTDs are available from links on http://www.nlm.nih.gov/databases/dtd/. The MEDLINE XML Element Descriptions document and the CatfilePlus and Serfile in XML Format Element Descriptions document will be edited to reflect these changes in the future. Licensees will be advised when sample files of XML records using the 2014 DTDs become available. NLM will announce changes in PubMed search functionality and display based on the 2014 DTD in the NLM Technical Bulletin later this fall after those decisions are final.

    1. Changes to NLMMedlineCitationSet DTD AND MEDLINE/PubMed XML
      The DTD changes for the 2014 production year are itemized in the Revision Notes section near the top of the DTD. The following describes the one substantive change to NLMMedlineCitationSet DTD and MEDLINE/PubMed XML:

      1. Include affiliation information for all authors.
        Until now, only the first author’s affiliation information was included in the MEDLINE record and the Affiliation element was part of the Article element. Beginning with the 2014 production year, citations will include all affiliation information published in the article. To associate the affiliation and author information, the Affiliation element is moved to the Author element from the Article element.

        DTD:
        <!ELEMENT     Author (((LastName, ForeName?, Initials?, Suffix?) | CollectiveName),Identifier*,Affiliation?)>
        <!ATTLIST     Author ValidYN (Y | N) "Y">
        Sample XML: <AuthorList CompleteYN="Y"> <Author ValidYN="Y"> <LastName>Billings</LastName> <ForeName>J Andrew</ForeName> <Initials>JA</Initials> <Affiliation> Palliative Care Service, Massachusetts General Hospital and the Harvard Medical School Center for Palliative Care, Boston, Massachusetts, USA.</Affiliation> </Author> <Author ValidYN="Y"> <LastName>Bauman</LastName> <ForeName>Jessica</ForeName> <Initials>J</Initials> <Affiliation> Division of Hematology and Oncology, Dana-Farber Cancer Institute, Boston, MA 02215</Affiliation> </Author> <Author ValidYN="Y"> <CollectiveName>Massachusetts General Hospital Palliative Care Nurse Champions</CollectiveName> <Affiliation>Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114</Affiliation> </Author> </AuthorList>

    2. Changes to NLMCatalogRecordSet DTD and CatfilePlus and Serfile XML
      The DTD changes for the 2014 production year are itemized in the Revision Notes section near the top of the DTD. The only DTD change for the 2014 production year is the date change from January 1, 2013 to January 1, 2014. There are no changes to CatfilePlus and Serfile XML.

  2. MEDLINE/PUBMED DATA CHANGES FOR THE NLM 2014 PRODUCTION YEAR
    1. Existing Affiliation data is moved from Article element to Author element and Affiliation data is possible for more than just the first Author. Also, Affiliation data is now possible for more than just the first Investigator if provided by the publisher in the data submission.

    2. The <DataBankList> envelope and its <Databank>, <DataBankName>, <AccessionNumberList>, and <AccessionNumber> elements contain information pertaining to the registration of several types of data including molecular sequence data, clinical trial numbers, gene expression/molecular abundance data, and PubChem identifiers. Currently, MEDLINE includes data from thirteen registries. Soon MEDLINE will include data from additional registries and the <DataBankName> list of valid values will be expanded. More information about the new Databanks will be published in the NLM Technical Bulletin at http://www.nlm.nih.gov/pubs/techbull/tb.html as well as in the documentation for licensees.

  3. FORTHCOMING 2014 BASELINE AND UPDATE FILES
    1. MEDLINE/PubMed
      After NLM completes its annual database maintenance activities, we expect to release the 2014 baseline files for MEDLINE/PubMed maintained with 2014 MeSH vocabulary and other changes to renewing licensees in mid-December (on or about December 17 or 18 -- within 24 to 48 hours after the release of the 2014 PubMed system). Daily update files for the 2014 production year will also begin at this time. A complete baseline reload to replace all previously received 2013 production year data ensures you have the most current and accurate version of all records and is required per Appendix C of the License Agreement for NLM Data.

    2. CatfilePlus and Serfile in XML
      The CatfilePlus and Serfile XML baseline files, also maintained with 2014 MeSH vocabulary and other global changes are expected on or about November 26, 2013.

    3. CatfilePlus and Serfile in MARC format
      MARC-formatted CatfilePlus and Serfile baseline files maintained with 2014 MeSH vocabulary and other global changes resulting from annual maintenance are expected on or about January 6, 2014. The last monthly files which reflect the 2013 MeSH vocabulary will be dated November 1, 2013. Appropriate LocatorPlus records which are updated as part of annual maintenance will be distributed to licensees in the files dated December 1, 2013. All MeSH headings in records distributed in the December 1, 2013 files will conform to 2014 MeSH.

    4. Catfile in MARC format
      MARC-formatted Catfile baseline files maintained with 2014 MeSH vocabulary and other global changes resulting from annual maintenance are expected on or about January 6, 2014. The last weekly file which will reflect the 2013 MeSH vocabulary is the file dated November 14, 2013. Appropriate LocatorPlus records which are updated as part of annual maintenance will be distributed to Catfile licensees in files beginning November 28, 2013. All MeSH headings in records distributed as of November 28, 2013 will conform to 2014 MeSH.

    5. Other databases
      As routine, all XML files distributed to licensees during 2014 for CCRIS, ChemID Subset, DIRLINE®, Gene-Tox, HSDB®, and TOXLINE® Subset will be complete replacement files. New files, if available, will be on the server for licensees on or about the 28th of the month. Some of these databases are updated irregularly and/or infrequently.

  4. SCHEDULE CHANGES FOR DAILY MEDLINE/PUBMED UPDATE DISTRIBUTIONS IN NOVEMBER 2013
    As is the case each year, in mid-November NLM will suspend distribution of new and revised MEDLINE/PubMed records in MedlineCitation Status = MEDLINE, MedlineCitation Status = PubMed-not-Medline, and MedlineCitation Status = OLDMEDLINE as preparations are made for the new production year. The last records in these three statuses, as well as PMIDs of records to delete, for the current 2013 production year are expected to be available Wednesday, November 20. Not later than Tuesday, November 26, NLM will begin to export only records in In-process and In-Data-Review status until availability of the MEDLINE/PubMed 2014 baseline files in mid-December (on or about December 17 or 18). Daily update files containing new and maintained records in all statuses and PMIDs of deleted records will commence upon release of the baseline files to licensees.

  5. CONTINUING TO LEASE NLM DATA IN 2014
    Licensees must confirm continued interest in leasing NLM data during the 2014 production year by renewing their license agreement following instructions that will be provided in November. Only those who renew will have access to the 2014 data, and licenses of non-responders will be terminated (and accordingly, access to the 2014 data will be denied). Per Section 13E of the License Agreement for NLM Data , licensees who cancel their license or whose license is terminated by NLM are to:
    1. Discontinue use of any promotional or other materials that refer to such data within thirty (30) days, and
    2. Cease use of data or information/data derived from data licensed under this license in all applications no later than ninety (90) days. Following that, licensees must promptly destroy and erase all data obtained under this license as well as any data contained in any derivative applications under the licensee’s control. (This does not apply to Catfile, CatfilePlus, or Serfile data.)

  6. INFORMATION PAGE FOR LICENSEES
    Please visit the NLM information page for licensees http://www.nlm.nih.gov/bsd/licensee/. Licensees should follow the links on this page for data element descriptions, update charts, announcements to licensees, and other documentation/resources relating to NLM leased data.

  7. LICENSE CODE REMINDER
    A unique alpha-numeric code including the letters "NLM" is assigned to each license and appears at the top of license-related e-mails sent by NLM. Please keep a record of your license code and reference it when corresponding with NLM about matters relating to your license or leased databases.


Computer Retrieval of Information on Scientific Projects (CRISP) Sub-file No Longer Available via NLM Data License

July 3, 2013

The CRISP sub-file of toxicology-related research projects has been removed from the National Library of Medicine (NLM) TOXNET version of TOXLINE. Furthermore, NLM will no longer make this data available in XML format for data licensees. We will remove the CRISP data sub-file from the NLM FTP server no earlier than 30 days from the date of this announcement (i.e., not earlier than August 2, 2013).

CRISP data are now available in complete form from the NIH RePORTER system (http://projectreporter.nih.gov/reporter.cfm. The NIH RePORTER system is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions, maintained by the NIH, and a replacement for CRISP.


New NLMMedlineCitationSet DTD dated May 1, 2013 Now in Effect

June 19, 2013

The new NLMMedlineCitationSet DTD dated May 1, 2013 is in effect as of today, June 19, 2013. The DTD is available from a link on http://www.nlm.nih.gov/databases/dtd/. NLM is now using this new DTD to create new and revised MEDLINE/PubMed records. NLM will not recreate nor re-export the 2013 MEDLINE/PubMed baseline XML data. For more information about this new DTD and changes to MEDLINE/PubMed XML see the May 15, 2013 announcement below.


Scheduled Maintenance at NLM June 8, 2013 from 8 am to 5 pm ET

June 7, 2013

On Saturday June 8 from 8 am to 5 pm ET, licensees will be unable to download files from our public ftp sites. Furthermore, we will not be able to post new MEDLINE/PubMed update files on Saturday June 8, 2013. Instead these files will be posted to the ftp site at noon ET Sunday June 9, 2013.


Changes to NLMMedlineCitationSet DTD AND MEDLINE/PubMed XML

May 15, 2013

There are 2013 mid-year changes to the NLMMedlineCitationSet DTD used for MEDLINE/PubMed. The January 1, 2013 version of the NLMMedlineCitationSet DTD currently in effect will be replaced by a new DTD dated May 1, 2013. The new DTD will be used for creating new and revised MEDLINE/PubMed records beginning no earlier than 30 days from the date of this announcement (i.e., not earlier than June 14, 2013). The 2013 MEDLINE/PubMed baseline XML data will not be recreated nor re-exported with these mid-year changes. The forthcoming May 1, 2013 DTD is available from a link on http://www.nlm.nih.gov/databases/dtd/.

The DTD changes are itemized in the Revision Notes section near the top of the DTD. The following describes the substantive changes to NLMMedlineCitationSet DTD and MEDLINE/PubMed XML:

The PubModel attribute of Article element has a new valid value of “Electronic-eCollection.” The Electronic-eCollection PubModel is used for electronic-only journals that publish individual articles first and then later collect them into an “issue” that is typically called an eCollection. The ArticleDate is the date the individual article is published and the PubDate is the date the eCollection is published. Please see the description of the Article element at http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#article for more information about how these elements and attributes are used in the source area of the PubMed citation display.

The NlmCategory attribute of AbstractText element has a new valid value of “UNASSIGNED.” The UNASSIGNED NlmCategory is used for labels in structured abstracts that NLM has not yet mapped to one of 5 categories, i.e., BACKGROUND, OBJECTIVE, METHODS, RESULTS, or CONCLUSIONS. For more information on structured abstracts, please see http://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#abstract.


NLM now using RDA: Resource Description and Access for all original cataloging of modern material

April 11, 2013

On March 31, 2013 the NLM began use of RDA: Resource Description and Access for all original cataloging of modern material, replacing the Anglo-American Cataloguing Rules, 2nd edition (AACR2). Bibliographic records distributed by NLM will continue to contain a mix of RDA and AACR2 records as NLM will accept AACR2 copy without upgrading these records to RDA. Any new authority records created by NLM will follow RDA guidelines, regardless of the rules used to create the bibliographic data. For more information please visit the RDA section on the NLM Cataloging homepage http://www.nlm.nih.gov/tsd/cataloging/mainpge.html.


MeSH Unique Identifiers Length Expanding to Ten Characters

March 8, 2013

On April 15, 2013, the length of unique identifiers used in the MeSH vocabulary will expand to 10 characters. Details are discussed in the NLM Technical Bulletin article titled "MeSH Unique Identifiers: Length Expanding to Ten Characters" at http://www.nlm.nih.gov/pubs/techbull/ma13/ma13_mesh_ui_expand.html.


Catfile, CatfilePlus and Serfile MARC 2013 Baseline Files Now Available

January 7, 2013

The updated 2013 MARC base files for Catfile, CatfilePlus, and Serfile are available on the NLM FTP server. These base files are each complete in a single file. Loading the base files on an annual basis is optional for MARC subscribers. If you have correctly loaded each of the update files, there is no need to reload the base files. The MARC file containing all the bibliographic records deleted by NLM between January 1, 2012 and December 31, 2012, will be available no later than February 1, 2013. Licensees who are new recipients of NLM MARC bibliographic records in 2013, as well as ongoing licensees who are discarding their pre-2013 records and reloading with the 2013 base files, do NOT need the delete file. The records in this file were removed from the NLM database prior to the pull of the 2013 base files. If loading new baseline files, you should then load the 2013 update files dated after the date of the base files.


MEDLINE/PubMed Data Changes and More MeSH 2013 Modifications

December 17, 2012

MEDLINE/PUBMED DATA CHANGES

NLM will soon include author keywords in MEDLINE/PubMed citations. The keywords are written by authors and supplied by publishers. Author keywords will be exported in records for licensees in the Keyword element of KeywordList. The KeywordList Owner attribute for author keywords is NOTNLM, i.e., <KeywordList Owner="NOTNLM">. NOTNLM is defined as a valid value for KeywordList Owner attribute in the NLMMedlineCitationSet DTD but has not been used by NLM until now. The Keyword MajorTopic attribute for author keywords is N, i.e., <Keyword MajorTopicYN="N">. NLM will begin exporting author keywords no earlier than 30 days from the date of this announcement (i.e., not earlier than January 17, 2013).

MORE MESH 2013 MODIFICATIONS

Two changes were made to the current 2013 MeSH Vocabulary. The entry terms Esomeprazole and Nexium are removed from the descriptor Omeprazole. A new descriptor Esomeprazole Sodium with entry term Nexium is created. MEDLINE/PubMed records will be updated to reflect these changes and will be re-exported to licensees. Licensees who downloaded the 2013 MeSH Descriptor Records should download them once again. As a reminder, the MeSH Files Available to Download are at http://www.nlm.nih.gov/mesh/filelist.html.


2013 MEDLINE/PubMed Baseline Data; CatfilePlus and Serfile XML Baseline Files

December 11, 2012

  1. AVAILABILITY OF 2013 MEDLINE/PUBMED BASELINE DATA
    The 2013 MEDLINE/PubMed baseline files, which replace all previously distributed MEDLINE/PubMed data are now available for FTP. Licensees have been e-mailed the location of the FTP access instructions with additional information.

  2. 2013 UPDATE FILES
    The first group of 2013 update files and the special PMID list text file (see item 3 below) are also available. Please be sure to read the _notes.txt file that is on the server accompanying the first update file medline13n0718. Update files should be processed after the baseline files in ascending file name numeric sequence (see item 3 below for exception) to ensure that all new records are added and the most current and accurate version of each record is retained.

  3. ADDITIONAL PMID LIST FILE
    A text file containing PMIDs of records in MedlineCitation Status = In-Process and MedlineCitation Status = In-Data-Review that have been retained in the 2013 version of PubMed at the time the 2013 baseline files were loaded and that are not exported to licensees in the first batch of update files is available. These records will eventually be exported in update files as completed records in MedlineCitation Status = MEDLINE or MedlineCitation Status = PubMed-not-MEDLINE or as deleted PMIDs in DeleteCitationSet. Licensees who wish to create a database as close as possible to the record content in PubMed on December 10, 2012 will want to include these records now.

    The file, named SpecialPubMedPMIDList_2013.txt, resides in the update file directory. Licensees may use the Entrez Utilities to download the records using the list of PMIDs.

    *IMPORTANT*: If you elect to add these records to your version of MEDLINE/PubMed, they must be added to your 2013 MEDLINE/PubMed database either 1) immediately after the baseline files and before any update files or, 2) immediately after update files medline13n0718 through medline13n0732 to ensure retaining the most current version of those records as subsequent update files are loaded. Do not add the records identified in SpecialPubMedPMIDList_2013.txt after you have processed medline13n0733 as this may result in retention of an earlier and inaccurate version of the records.

  4. 2012 MEDLINE/PUBMED FILES TO MOVE TO NEW DIRECTORY
    The 2012 update files are moved to a new directory where they will remain for several weeks. Contact NLM at nlmdatadistrib@nlm.nih.gov if you need access to those files.

  5. DOCUMENTATION
    Documentation for the MEDLINE/PubMed baseline database is available from links in the Data Availability and Maintenance section of NLM’s information page for MEDLINE/PubMed licensees. Also see the MEDLINE/PubMed Maintenance Overview for information about and points to consider for processing update files. Announcements during the year will be added as they become available.

  6. MEDLINE/PUBMED BASELINE REPOSITORY (MBR)
    The 2013 baseline data will be included at a later date in the MEDLINE/PubMed Baseline Repository (MBR) resources. If you wish to search the baseline data via the MBR Query Tool, be sure to use the same IP address registered with NLM for access to MEDLINE/PubMed from NLM’s FTP server.

  7. MeSH 2013 MODIFICATIONS
    Two changes were made to the current 2013 MeSH Vocabulary. The descriptor Tropical Diseases was removed and the descriptor Tropical Medicine was returned to its 2012 content. If you downloaded the 2013 MeSH Descriptor Records prior to 12/11/2012 you should download them again. As a reminder, the MeSH Files Available to Download are at http://www.nlm.nih.gov/mesh/filelist.html.

CatfilePlus and Serfile XML Baseline Files

The updated XML base files for CatfilePlus and Serfile are available on the NLM FTP server. CatfilePlus is in 4 parts, named "catplusbase1of4.2013.xml", "catplusbase2of4.2013.xml", etc. The Serfile base file is complete in a single file, named "serfilebase.2013.xml". The baseline files contain all records through November 16, 2012 and should be used to completely replace all records previously distributed. The first XML update files for CatfilePlus and Serfile were made available November 23, 2012.