Indexing Journal Articles in Biomedical Literature, NLM

The Cygnus biomedical indexing team prepares biomedical and scientific bibliographic citations for entry into national and international databases. This includes our long-running work for MEDLINE®, the National Library of Medicine’s (NLM) premier bibliographic database that is the primary component of PubMed®. PubMed comprises more than 20 million citations for biomedical literature from MEDLINE® life sciences journals, and online books, with and 3,000-5,000 references added daily. 

Cygnus provides high-quality indexing services to NLM and assisted in the review, correction, and enhancement of bibliographic citation data for MEDLINE®. Cygnus presently provides MeSH indexing for some 124,000 biomedical journal articles annually in English, Spanish, and 12 other foreign languages, with a 99.8% acceptance rate. Led by our Senior Medical Librarian, our staff of indexing professionals all have advanced scientific degrees and are experienced in researching, identifying, reviewing and indexing scientific literature for MEDLINE. In addition, Cygnus has worked closely with NLM on the Medical Text Indexer Frontline (MTIFL) Pilot Study to determine the feasibility of substantial automation of the indexing process.

Our role in this process ensures that researchers around the world can find, review, and incorporate today’s most up-to-date scientific knowledge into their research projects. Each member of our indexing team has advanced scientific degrees and substantial indexing and scientific pedigrees. Most hold Ph.D.’s and/or M.D.’s in relevant biomedical disciplines and a minimum of 5 years of indexing experience.  The combination of high level scientific expertise, seasoned indexing experience, and diverse language fluency are the formidable attributes which distinguishes our services and which have led to our yearly increased production and consistent accuracy for descriptive indexing.


This contract requires the services of medical librarians, scientists and consumer health care specialists who must research and analyze subject content from biomedical journals and articles and ensure that each record is transmitted to NLM with all necessary data to verify the accuracy and authoritativeness of the information. The capabilities required include some of the following:

  • Biomedical subject matter expertise
  • Indexing, abstracting and cataloging services
  • Translation and transliteration services
  • Database development
  • Data formatting

The major activities of the contract include the following items:

  • Annually indexing over 125,000 biomedical publications with a 99.8 percent acceptance rate.
  • Responding to NLM requests to revise indexes created by other contractors because of lower quality.
  • Performing descriptive indexing of foreign language medical journal articles using Medical Subject Headings (MeSH), Supplementary Chemical Records, MEDLARS (Medical Literature Analysis and Retrieval System) Indexing Manual, Technical Notes, Technical Memoranda, and Translation Memoranda.
  • Ensuring that each record transmitted to NLM includes all necessary data, such as pagination, author, author affiliation, title, vernacular title, and research grant support.
  • Verifying foreign language codes.
  • Providing English translations of titles and authors= names for each article printed in the Cyrillic alphabet.  Provides transliterations of authors= names printed in Japanese and Chinese.
  • Analyzing subject content of each article and assigns descriptors, check tags, and qualifiers selected from MeSH and Index Medicus.
  • Assigning Medical Subject Headings. For our current NLM indexing contract, the indexers consistently scrutunize MeSH terminology to recommend revisions to existing terms and add new vocabulary to improve MeSH’s search capabilities. Our indexers routinely create descriptions, annotations, scope notes, synonyms (entry terms), allowable qualifiers, history notes, and hierarchy placement for these rare diseases. As part of the indexing process, our indexing team also uses the MTI’s recommendations to complete records.
  • Using Subheadings/Qualifiers. Cygnus indexers also select the appropriate subheadings or qualifiers for each index term. Our indexers consult the hierarchical list of allowed qualifiers that is provided in the record for each term and displayed in the subheadings menu of the DCMS. They also consult the MeSH record to identify the appropriate subheading directions for each term, and will select the subheadings most relevant to the content of the article, thereby narrowing the selection to two or three subheadings per term.
  • Validating records to prevent errors, such as misspellings, typographical errors, and validation of words in the title and abstract of the article appear in a dictionary file. Words that do not appear in the dictionary are highlighted for further action by the indexer, who either must correct the misspelling or override the warning. Validation of the correctness of entire bibliographic citations by Cygnus indexers will include determination of:
    • Authors’ names (all authors’ names have to present in the order they appear in the text): make sure that surname appears first follows by first name.
    • Authors’ affiliation: the affiliation for the first author should be present, (if not included, check the abstract, introduction, or discussion section of the article).
    • Titles: check the title with original.
    • Pagination: check to ensure that it corresponds with the articles.
    • Abstracts: check the original abstract (paper copy or online) with the abstract in DCMS to ensure that the created citation includes an abstract (sometimes the abstract is incomplete or is missing; in this case, if only a few words are missing, the indexer is responsible for completing the abstract; however, if the whole abstract is missing, the indexer flags the article and the corrections are done in-house).
    • Grammar: This rules applies to English and non-English articles! Indexers are responsible to make appropriate corrections in titles, authors’ names, authors’ affiliations, pagination, and abstracts.
    • Common mistakes: Correction of common mistakes such as this example:”Women health in chinese community”. The word “Chinese” should be capitalized.


Cygnus has successfully supported NLM mission by increasing its productivity at the request of NLM without impacting the total cost of the project. We are currently indexing approximately 124,000 publications annually, an increase from 115,000 in previous years. We continue to meet all contract schedules and budget estimates as required under the contract.

To maintain our high quality standards, Cygnus’s Project Manager monitors staff production quotas weekly and makes any necessary adjustments to respond to staffing and production challenges. We carefully monitor our weekly output to ensure that we adhere to NLM’s production guidelines for overall production quotas, and prevent overproduction.

Cygnus has retained a growing population of dedicated and talented staff. It is not by accident that five of our high-volume staff has worked for Cygnus for at least 10 years. In addition, six of our high-volume staff has worked for us for six or more years, and six others of our high-volume staff have been with us for at least three years. Key to our staff retention and high performance is the continued education of our staff to ensure they remain current with the continuing indexing improvements, memorandum, technologies, and changing priorities. We focus on nurturing our freelance staff as well as our full time employees. Retaining personnel and identifying new candidates are key services Cygnus provides to support NLM’s indexing requirements.

Over the course of our indexing, NLM has constantly struggled with balancing the need for greater productivity with limited resources. With our current contract, Cygnus has offered NLM discounted rates for increased productivity to help with this balance. This arrangement is not based on escalating our revenue, but is an example of how as an NLM partner, we can assist in helping maintain the balance of productivity and cost.  We value NLM’s mission and we willingly cooperate in many ways that go above and beyond. 

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