MEDLINE® Data Changes 2010
At this time each year the NLM Technical Bulletin traditionally includes information about changes made to MEDLINE during annual National Library of Medicine® (NLM®) maintenance known as Year-End Processing (YEP). This article collects, in one place, the notable data changes for 2010. Some topics may be linked to another article where details will be found. For information about how this maintenance affects the NLM schedule for adding indexed MEDLINE citations to PubMed®, see the article, MEDLINE® /PubMed® Year-End Processing Activities.
Two additional resources, Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2009 and Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information, include examples of typical changes that take place in MEDLINE citations during YEP.
MeSH® Vocabulary Updated for 2010
The MeSH Browser currently includes a link to the 2010 MeSH vocabulary. Searchers should consult the Browser to find MeSH headings of interest and their relationships to other headings. The Browser contains MeSH Heading records that may include scope notes, annotations, entry terms, history notes, allowable qualifiers (subheadings), previous headings and other information. It also includes Subheading records and Supplementary Concept Records (SCRs) for substances that are not MeSH Headings.
The MeSH Tree Structures are also available online in both PDF and HTML formats with all indented terms showing.
For highlights about 2010 MeSH see the forthcoming article, What's New for 2010 MeSH.
The PubMed MeSH database and translation tables will also be updated to reflect 2010 MeSH in mid-December when YEP activities are complete and the newly maintained MEDLINE data are available in PubMed.
Updated MeSH in MEDLINE Citations
MEDLINE records with updated MeSH will be in PubMed in mid-December 2009. See the Changing Saved Searches Quick Tour for details on revising My NCBI saved searches.
The MeSH Section homepage provides links to descriptions of MeSH maintenance. The About Updates link under the "MEDLINE Citation Maintenance" section explains how NLM prepares the changes in a machine-readable form for others to use. To access the XML files for the tasks processed for this maintenance, click on the "Download XML Files" link under this same section; the 2010 changes should be available sometime in January 2010. This information is helpful for those individuals or organizations using MeSH headings in their own application (such as indexing curricula guides) and want to update those applications with the new version of MeSH.
New MeSH Headings
This year 422 new MeSH Headings were added.
Typically, NLM does not retrospectively re-index MEDLINE citations with new MeSH Heading concepts. Therefore, searching PubMed for a new MeSH term tagged with [mh] or [majr] effectively limits retrieval to citations indexed after the term was introduced. PubMed Automatic Term Mapping (ATM) expands an untagged subject search to include both MeSH Terms and All Fields index terms and may retrieve relevant citations indexed before the introduction of a new MeSH term. Searchers may consult the MeSH Browser or the MeSH database to see the Previous Indexing terms most likely used before the new MeSH Heading was introduced.
Brand New Concepts
Examples of new MeSH headings of special interest to searchers are highlighted below by Category. You can browse all of the new 2010 concepts on the MeSH New Descriptors Web page.
- Category A - Anatomy
- Bacterial Structures
- CA1 Region, Hippocampal
- CA2 Region, Hippocampal
- CA3 Region, Hippocampal
- Cervical Rib
- Fungal Structures
- Germ Cells, Plant
- Uterine Artery
- Viral Structures
- Category B - Organisms
- Human T-lymphotropic virus 3
- Influenza A Virus, H1N2 Subtype
- Proboscidea Mammal
- Simian T-lymphotropic virus 3
- Uropathogenic Escherichia Coli
- Category C - Diseases
- Alien Hand Syndrome
- Anterior Wall Myocardial Infarction
- Asthma, Aspirin-Induced
- Contrecoup Injury
- Corpse Dismemberment
- Inferior Wall Myocardial Infarction
- Latent Tuberculosis
- Leprosy, Multibacillary
- Leprosy, Paucibacillary
- Obesity, Abdominal
- Pelvic Organ Prolapse
- Additionally a number of Rare Disease terms were added.
- Category D - Chemicals and Drugs
- Antibodies, Neutralizing
- Behind-the-Counter Drugs
- Dentin Desensitizing Agents
- Histone Deacetylase Inhibitors
- Neuronal Tract-Tracers
- Ubiquitinated Proteins
- Category E - Analytical, Diagnostic and Therapeutic Techniques and Equipment
- Animal Assisted Therapy
- Cathode Ray Tube
- Child Restraint Systems
- Compassionate Use Trials
- Delayed Diagnosis
- Early Termination of Clinical Trials
- Electronic Health Records
- Enzyme Replacement Therapy
- Epicardial Mapping
- Equine-Assisted Therapy
- Health Records, Personal
- Individualized Medicine
- Insecticide-Treated Bednets
- Molecular Imaging
- Mosquito Nets
- Off-Label Use
- Patient Positioning
- Preoperative Period
- Recreation Therapy
- Single Embryo Transfer
- Category F - Psychiatry and Psychology
- Emotional Intelligence
- Information Seeking Behavior
- Category G - Biological Sciences
- Adaptive, Immunity
- Bacterial Shedding
- Climate Change
- Colony Collapse
- Cross Protection
- Endangered Species
- Gametogenesis, Plant
- Genetic Loci
- Global Warming
- Immune Evasion
- Immunity, Humoral
- Microbial Interactions
- t-Complex Genome Region
- Viral Tropism
- Virus Release
- Category H - Natural Sciences
- Advanced Practice Nursing
- Chemistry, Analytic
- Sleep Medicine Specialty
- Travel Medicine
- Category I - Anthropology, Education, Sociology and Social Phenomena
- Health Literacy
- Independent Living
- Medical Tourism
- Category J – Technology, Industry, and Agriculture
- Automation, Laboratory
- Fast Foods
- Food, Preserved
- Functional Food
- Category K – Humanities
- Therapeutic Equipoise
- Therapeutic Misconception
- Category L - Information Science
- Biometric Identification
- Data Mining
- Search Engine
- Webcasts as Topic
- Category M - Named Groups
- Category N - Health Care
- American Recovery and Reinvestment Act
- Comparative Effectiveness Research
- Drug Recalls
- Economic Development
- Economic Recession
- Medical Device Recalls
- Post-Exposure Prophylaxis
- Product Recalls and Withdrawals
- Safety-Based Drug Withdrawals
- Safety-Based Medical Device Withdrawals
- Category Z - Geographicals
- Democratic People’s Republic of Korea
- Ottoman Empire
- Republic of Korea
Changes to MeSH Headings
Changes to citations of particular interest include:
- In 2010, the new heading Eukaryota was created and added to the MeSH vocabulary. The Protozoa tree was disassembled and the vast majority of newly created taxonomic headings and headings previously treed under Protozoa are retreed under various groups under Eukaryota.
- Plant Components and Fungal Components (formally treed in the B tree) are renamed Plant Structures and Viral Structures and re-treed in the A tree.
- Hepatitis, Toxic is replaced by Drug-Induced Liver Injury and Hepatitis, Chronic, Drug Induced is replaced by Drug-Induced Liver Injury, Chronic.
- Food Poisoning is replaced by Foodborne Diseases.
- Hemorrhagic Disease of the Newborn is replaced by Vitamin K Deficiency Bleeding.
- Monsters is replaced by Abnormalities, Severe Teratoid.
- Antibiotics, Antifungal is replaced by Antifungal Agents.
- Genetic Screening is replaced by Genetic Testing.
- Cyclones is replaced by Cyclonic Storms.
- Cytology is replaced by Cell Biology.
- Mass Immunization is replaced by Mass Vaccination.
- Chemistry, Analytical is replaced by Chemistry Techniques, Analytical.
In addition to the replaced-by heading changes, YEP includes other adjustments to MEDLINE citations to reflect 2010 MeSH vocabulary and to enhance search retrieval. These follow-on adjustments are largely the adding of more MeSH headings or Supplementary Concept Record Names of Substances (NM) to citations to help searchers refine retrieval. In some cases, the changes clarify areas where a single concept existed before, but it is now represented by two or more specific concepts.
These types of changes, along with others documented on the Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information Web page, suggest the importance of routinely using the PubMed Details feature when searching to see how terms are mapped with the new year's vocabulary and then checking the MeSH Browser or the MeSH database for clarification. Additional information is also available in the article, Skill Kit: The Effects of Year End Processing (YEP) on Saved Searches or RSS Feeds.
Two New Publication Types for 2010
For 2010, NLM will begin using two new Publication Types, Webcasts and a new research support publication type Research Support, American Recovery and Reinvestment Act.
Notable MeSH Changes and Related Impact on Searching
The old Protozoa heading was deleted and replaced in 2010 by Eukaryota. Protozoa now maps to the subheading /parasitology. Protozoa and its indentions were also indexed with Animals in the past. This coordination is no longer in effect for 2010 MeSH for the heading Eukaryota and its indentions. Precoordinated headings related to protozoa still exist in 2010 MeSH, e.g.;
- Antibiodies, Protozoan
- Antigens, Protozoan
- DNA, Protozoan
- Genes, Protozoan
- Protozoan Infections
Hemorrhagic Disease of Newborn is replaced by Vitamin K Deficiency Bleeding; however, this term is coordinated with Infant, Newborn only if it is pertinent.
Immunity, Humoral is a new MeSH Heading and no longer an Entry Term to Antibody Formation.
Global Warming is a new MeSH Heading and no longer an Entry Term to Greenhouse Effect.
Economic Recession is a new MeSH Heading and no longer an Entry Term to Economics.
Korea is now defined as an historical geographic concept. Two new MeSH Headings are:
- Democratic People’s Republic of Korea (has an entry term of North Korea)
- Republic of Korea (has an entry term of South Korea)
The new MeSH Heading, Compassionate Use Trials, will not be routinely coordinated with any of the Clinical Trial Publication Types, unless the study design meets the MeSH definition of a clinical trial.
The Publication Type Webcasts will be used when the link to a Webcast is an integral part of an article, or if the Webcast represents the entire article.
Other changes that affect searching include:
- The MeSH Heading Rabbits has two new Entry Terms: Rabbits, New Zealand and Rabbits, Chinchilla.
Entry Combination Revisions
This year during YEP, NLM will again retrospectively replace certain MeSH heading/subheading combinations, known as Entry Combinations, with the new precoordinated MeSH heading. If you get no retrieval for a MeSH Heading/subheading combination check the heading in the 2010 MeSH Browser to see if the Entry Combination information indicates a different term.
Below are the eleven Entry Combinations new for 2010:
Previous MeSH Heading/Subheading
Replaced-by Heading for 2010
|Aminosalicylic Acid/analogs & derivatives||Aminosalicylic Acids|
|Argininosuccinate Lyase/deficiency||Argininosuccinic Aciduria|
|Caspase 8/deficiency||Alstrom Syndrome|
|Complement C1 Inhibitor Protein/deficiency||Hereditary Angioedema Types I and II|
|Cysteine Proteases/antagonists & inhibitors||Cysteine Proteinase Inhibitors|
|Exopeptidases/antagonists & inhibitors||Protease Inhibitors|
|Hepatitis, Chronic/chemically induced||Drug-Induced Liver Injury, Chronic|
|Histone Deacetylases/antagonists & inhibitors||Histone Deacetylase Inhibitors|
|Iduronate Sulfatase/deficiency||Mucopolysaccharidosis II|
|Liver Diseases/chemically induced||Drug-Induced Liver Injury|
|Methylmalonyl-CoA Decarboxylase/deficiency||Propionic Acidemia|
|Ornithine Carbamoyltransferase/deficiency||Ornithine Carbamoyltransferase Deficiency Disease|
|Serine Proteases/antagonists & inhibitors||Serine Proteinase Inhibitors|
Additional Changes to MEDLINE and OLDMEDLINE Data
- [Editor's Note: This sentence was corrected on December 14, 2009.]
Linking ISSN data will be included with the 2010 PubMed system:
The ISSN International Center assigned new Linking ISSN data which NLM added to most existing serial records in LocatorPlus® and to those journal article citations.
- [Editor's Note: This sentence was corrected on December 14, 2009.]
International Organization for Standardization (ISO) Abbreviations added to all serial records and to journal citations:
As a part of Year-End Processing, ISO Abbreviations were added to the serial records for indexed journals, and therefore, the citations for these journals will have ISO Abbreviations when the new system comes up in mid-December.
Cites will contain PMIDs and source data for items in the bibliography or list of references at the end of an article that is deposited in PubMed Central® (PMC). Cites will contain only PMIDs and source data for citations where an actual PMID for the cited article exists in the NLM Data Creation and Maintenance System (DCMS). It is therefore possible for a citation to be present in the list of references for an article and yet the PMID is not included in the Cites list because it is not present in the DCMS. Over 26.5 million Cites were added to 1,092,196 PubMed citations.
- New Granting Organization:
Canadian Institutes of Health Research was added in October 2009 as a granting agency.
- Wellcome Trust retrospective update:
On September 29, 2009 Wellcome Trust funding information was added to roughly 22,000 MEDLINE citations for articles published from 1984-1999.
- Language Code changes:
The Library of Congress MARC language codes for Croatian and Serbian languages have changed:
Croatian is now hrv; it was scr.
Serbian is now srp; it was scc.
NLM processed the changes for these languages on MEDLINE citations in mid-November.
Journal Subject Term changes for 2010
Two of the Subject Terms assigned to MEDLINE journals have changed as part of Year-End Processing changes for 2010 MeSH. The two changes are:
- Cytology was replaced by Cell Biology
- Chemistry, Analytical was replaced by Chemistry Techniques, Analytical
Tybaert S. MEDLINE® Data Changes 2010. NLM Tech Bull. 2009 Nov-Dec (371):e8.