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MEDLINE Data Changes - 2002
his time of year the Technical Bulletin traditionally includes information on changes made to MEDLINE during annual National Library of Medicine (NLM) maintenance known as Year-End Processing. For information on how this maintenance affects NLM's schedule for adding indexed MEDLINE citations to PubMed®, see the article, MEDLINE/PubMed End-of-Year Activities in this issue.
- The annual update to Medical Subject Headings (MeSH®), NLM's controlled vocabulary used for subject indexing and retrieval
- Updated MeSH in MEDLINE citations to reflect changes in MeSH vocabulary
- New Author Name indexing policy
- Other indexing policy changes
- Other changes to data in MEDLINE citations including EC/RN, Publication Type, Title Abbreviation and ISSN information
The MeSH Section's MeSH Browser currently contains 2001 MeSH with a link to a version with the 2002 MeSH. Searchers should consult the MeSH Section's MeSH Browser to find descriptors of interest and to see these in relationship to other descriptors. The Browser displays virtually complete MeSH records, including the scope notes, annotations, entry vocabulary, history notes, allowable qualifiers (subheadings), etc. It also provides links to relevant sections of the NLM Indexing Manual. For details about 2002 MeSH changes, see the article, What's New for 2002 MeSH in this issue.
It is expected that PubMed's MeSH Browser and translation tables will be updated to reflect 2002 MeSH in January when end-of-year activities are complete and the newly maintained MEDLINE is available via PubMed.
Updated MeSH in MEDLINE Citations
- Changes to MeSH Terms
During year-end processing, all MeSH Terms in MEDLINE citations are updated to reflect changes in 2002 MeSH. These changes are expected in PubMed by January.For example, the MeSH Heading "Hog Cholera" has been changed to "Classical Swine Fever" in 2002 MeSH. MEDLINE citations indexed from 1966-2001 containing the MeSH Term "Hog Cholera," will all be changed to "Classical Swine Fever."
Remember that the mapping of see references can also change. For example, "Allspice" has been removed as, "See Rosales." For 2002, it is "See Pimenta" which has the History note of "2002; use Rosales 1998-2001, use SPICES 1993-1997."
- New MeSH Terms
Eight hundred and forty-seven (847) new MeSH Subject Headings have been introduced in 2002 MeSH.New MeSH terms may begin to appear on MEDLINE citations by January. See the article, Hands-On: Revising PubMed Cubby Stored Searches in this issue for details on changing Cubby stored searches to reflect changes in MeSH.
Please note that there are several new food hypersensitivity terms including:
- Egg Hypersensitivity
- Nut Hypersensitivity
- Peanut Hypersensitivity
- Wheat Hypersensitivity
Other new disease headings include:
- Coronary Stenosis
- Coronary Restenosis
- Metabolic Syndrome X
New organism-specific proteins include:
- Zebrafish Proteins
- Fish Proteins
- Saccharomyces cerevisiae Proteins
- Schizosaccharomyces pombe Proteins
- Caenorhabditis elegans Proteins
- Xenopus Proteins
- Amphibian Proteins
- Arabidopsis Proteins
- Soybean Proteins
- Avian Proteins
- Drosophila Proteins
Generally, NLM does not retrospectively index MEDLINE citations with new MeSH Headings. Therefore, searching for a new MeSH Term qualified as [MeSH Term] or [Major MeSH Topic] effectively limits retrieval to citations indexed after the term was introduced. An unqualified subject search in PubMed expands a search by including both MeSH Term and Text Words, and may retrieve relevant citations indexed before the introduction of a new MeSH Term.
For example, a new MeSH term, "Echinacea" was introduced in 2000 MeSH. A PubMed query for "echinacea" qualified as [MeSH Term] yields 54 citations, indexed from 2000 through October 2001. A simple, unqualified PubMed query for "echinacea" yields 147 citations from 1966 through October 31, 2001.
- Other MeSH Changes
All citations indexed prior to the 2002 indexing year with a specific term in the Plants, Toxic tree (B06.660) or the Plants, Medicinal tree (B06.560) will have their parent heading (i.e., Plants, Toxic or Plants, Medicinal) added retrospectively. For example, any citation indexed with the MeSH heading, Garlic, will have the MeSH heading Plants, Medicinal added if it is not already present in the citation.All indentations of specific plant names have been removed from these two trees for 2002 MeSH. Indexers will now coordinate index when these aspects are important to the article. In the past, indexers did not add the parent term to the citation when using an indented heading to describe the article because the explosion search capability would retrieve the citations. Now that these two trees no longer explode, adding the parent heading to the citation for retrospective data and using coordinate indexing for 2002 forward provides the same retrieval capability that explosion did.
Because of new capabilities available with the re-invented citation maintenance system, NLM was able to do some verification of various entry combinations over time. In the past when a precoordinated heading was introduced to replace a MeSH heading/subheading combination for prospective indexing, maintenance of retrospective citations was not performed. This year during year-end processing, NLM replaced the illegal MH/SH combinations on older citations with the legal, precoordinated MeSH heading (e.g., the illegal combination Aorta/radiography was changed to Aortography).
Please note - these headings were added with asterisks to designate the main point of an article when appropriate but no subheadings can be added retrospectively.
The MeSH heading Coronavirus, Human was deleted and all occurrences of that term were replaced by the MeSH heading, Coronavirus. In addition, maintenance tasks were performed to find those citations pertaining to two specific coronaviruses - 229E and OC43. When appropriate, the new MeSH headings Coronavirus 229E, Human and/or Coronavirus OC43, Human were also added to those citations.
The MeSH heading Diarrhea Virus, Bovine Viral was deleted and all occurrences of that term were replaced by the MeSH heading, Diarrhea Viruses, Bovine Viral. In addition, maintenance tasks were performed to find those citations pertaining to two specific bovine diarrhea viruses - 1 and 2. When appropriate, the new MeSH headings Diarrhea Virus 1, Bovine Viral and/or Diarrhea Virus 2, Bovine Viral were also added to those citations.
The MeSH heading Papovaviridae was deleted and two new headings have been introduced to cover this concept. Maintenance tasks were performed to add both new headings (Papillomaviridae and Polyomaviridae) to all citations with occurrences of the old heading, Papovaviridae.
Beginning with 2002 publication dates, NLM will enter full author names for MEDLINE citations. This new policy will apply to the following fields:
- Author (AU)
- Personal Name as Subject (PS)
- Investigator Name (IR) - Note: This field only appears on MEDLINE citations created or maintained by one of our collaborating data producers, the National Aeronautics and Space Administration (NASA).
Full author names are entered when they appear in the author position of an article, usually on the title page of an article. If only the last name and initials appear in the author position, then only the last name and initials will be entered even if a fuller form of the name appears elsewhere in the article or in the Table of Contents for the journal.
Full author names are currently present on all citations created by another collaborating data producer, the Kennedy Institute of Ethics (KIE), regardless of publication date.
- Author Searching in PubMed
For now, full Author Names will not be searchable in PubMed. Searching author names in PubMed remains the same using last name plus two initials and suffix if appropriate. PubMed's MEDLINE and XML display formats will show the full names when present. Additionally, full author names will not be printed in Index Medicus. - Author Initials
Even with the new 2002 policy of capturing full author name, NLM will continue its policy of using only two initials for searching in PubMed as explained above. Initials data are generated from the Data Creation and Maintenance System (DCMS) ForeName data element using an algorithm which was reviewed and adjusted as part of our year end activities. Here are the highlights of that algorithm:- When the ForeName data element consists of only initials, there are spaces between initials.
- Only 2 initials are generated. Initials are at the beginning of the name string or following a break. A break is a space or hyphen. Only capital letters in the ForeName elements are candidates for initials except for the letter following a hyphen. The letter following a hyphen is a candidate for an initial unless the string following the hyphen is "ichi".
- An initial includes its associated particle. Current particle values are: da, de, del, do, dos, du, el, el-, and le. All except "el-" are followed by a space and are preceded by a space or are at the beginning of the name string. Checking for particles is not case sensitive. If found, all particles are converted to lower case when generated as part of the Initials data element.
- If the language of the article is Bulgarian, Russian, Serbo-Croatian (Cyrillic), or Ukranian, then one initial may be represented by a 2-(or in one case a 4-)character, mixed-case transliteration into the Roman alphabet. Current, mixed-case transliteration values are: Dj, Lj, Nj, Ch, Sh, Iu, Ia, Ie, Zh, Kh, Ts, Dz, Shch.
Here are some examples:
Last Name Fore Name Initials Sarhan A R AR Gonzales-loza Maria del R Mdel R Gonzales-loza M del R Mdel R Dubuisson Jean-Bernard JB Amara Mohamed el-Walid Mel-W Shan Yu-fei YF Taylor David S I DS Krylov Ia K IaK
Note that the end result of generating the Initials data is that the two initials are closed up with no space between, even though there might be spaces elsewhere in the Initials string if one or both of the initials has embedded spaces.
There are some author names that have no initials. Mostly these are Malaysian names where the entire name is entered in the LastName DCMS data element.
Articles discussing therapies using plants or preparations from plants are indexed with the MeSH heading, Phytotherapy, a new heading for 2002. Studies involving plants for therapy will be indexed as follows:
- Phytotherapy
- disease/drug therapy
- specific plant
- Plant Preparations (or one of its more specific terms)/therapeutic use
- plant chemical/therapeutic use (if discussed)
Phytotherapy is reserved for articles in which the plant itself, an extract of the plant, or the plant chemical whose structure has not yet been determined is used therapeutically. Many therapeutic agents used in medicine today are derived from plants. Their chemical structure and pharamacologic properties have been well characterized and their therapeutic value firmly established. The MeSH heading Phytotherapy will not be used in those cases; for example, an article discussing the treatment of ovarian cancer with paclitaxel. Paclitaxel was originally isolated from the Pacific Yew tree and its structure and pharmacologic properties are well known and it can now be chemically synthesized. This article would be indexed with the following headings - notice that Phytotherapy is not used:
- Ovarian Neoplasms/drug therapy
- Paclitaxel/therapeutic use
- Antineoplastic Agents, Phytogenic/therapeutic use
- a heading from the Plants [B6] tree with either therapeutic use or administration & dosage attached as a subheading, or
- the heading Antineoplastic Agents, Phytogenic with either therapeutic use or administration & dosage attached as a subheading AND a heading from the Plants [B6] tree [corrected], or
- a heading from the Angiosperms [B6.388.100] tree AND a heading from the Complementary Therapies [E2.190] tree
- New Publication Type - Patient Education Handout
Some clinical journals have begun adding "patient pages" that relate to substantive articles. The "patient pages" are designed for physicians to share with their patients or use as talking points with patients. Many searchers expressed interest in being able to restrict to this type of article. The new publication type Patient Education Handout will allow users to limit this way.
- Supplementary Concepts: EC/CAS Registry Numbers [EC/RN]
Changes in 2002 MeSH also require changes to some EC/RN data, including Substance Name [NM], in MEDLINE citations during year-end processing. These affect not only the MeSH chemical concepts in category D, but the Supplementary Concepts as well.
- Identification of Clinical Trials in MEDLINE
For the seventh year, NLM continued its work with the Cochrane Collaboration to enhance the identification of clinical trials in MEDLINE. For 2001 maintenance, the Cochrane identified over 7,200 MEDLINE citations to articles published from 1966-2001 to which the Randomized Controlled Trial or Controlled Clinical Trial Publication Type has been added. (Over 5,000 MEDLINE citations were similarly enhanced during 2000 maintenance.)
- Citation Subset Values Added to MEDLINE Records
Citation subset values X, E, Q, and S were added to the MEDLINE records that had also been included in the former AIDSLINE, BIOETHICSLINE, HISTLINE and SPACELINE databases, respectively. These values ensure that the PubMed Journal Citation Subsets (i.e., jsubsetx, jsubsete, jsubsetq, jsubsets) include all citations that were in the former databases, whether the citations were unique to the database, or derived from other databases (e.g., MEDLINE, HealthSTAR). Prospectively, collaborating indexers may add these citation subset values to new MEDLINE citations. Searchers should note that citation subset values are multiply occurring which means that individual citations may be included in several subsets, including the Index Medicus one (jsubsetim).
- Miscellaneous Changes and Corrections
Abstract copyright statements may be supplied electronically by publishers to be included in MEDLINE records. The data are to reside in the DCMS CopyrightInformation data element. However, on some records the copyright information was appended at the end of the Abstract data element instead. Maintenance tasks were performed to move this information to the correct data element when necessary.Maintenance activities also included verifying and/or correcting publication type assignments on MEDLINE citations and updating grant acronym information to reflect those currently used by NIH institutes.
MEDLINE® Data Changes - 2002. NLM Tech Bull. 2001 Nov-Dec;(323):e11.
