Search Options/Glossary (Literature)

The Literature dataset focuses on publication and preprint fields. You will find article-specific details such as doi, publication year, source (journal name or preprint server), and citations, as well as some linked grant record and clinical trial data. Below is a glossary of terms that can be found in the Literature dataset (search fields, record view, export, and more) along with example search criteria. 

To learn more about how to search using search fields, visit the Search Strategies section. Note: When performing a manual query, search fields can be selected by clicking the Search Fields button below the Search icon in the search bar. If a field is not displayed in the list, you can still search it by using a Custom Field.

Abstract: This is a concise summary of the article. Topics captured in the abstract help with indexing literature. If using this as a search field, you can search for terms or phrases in the abstract. 

Example:Signaling

AI labels: These are the AI labels for clusters across the different display levels (broad, intermediate and narrow). You can use this field to search for terms or phrases in the labels. Read more about the AI labels.

  Example:Antibodies

Animal: This is the percentage of the article’s MeSH terms counted as Animal research. This is shown as a score between 0 and 1, with 1 being equivalent to 100%, meaning all terms from the article are Animal. See more on this methodology.

Example:1

Appl ID: (For linked Grants) This is the specific application identifier of the grant record. It is unique to any applications submitted for a grant record. This field is available for literature linked to grant records only.

Example:8901196

APT Score: The Approximate Potential to Translate (APT) score identifies early signatures of bench-to-bedside translation and is calculated using machine learning. Possible values are 5%, 25%, 50%, 75%, and 95%. APT has been calculated historically where data is available. If there are no MeSH terms, the APT will be N/A. Find more information about the iCite Translation module.

Example:25%

Article Citation Rate (ACR): The ACR is the number of times a publication is cited per year. It is used to calculate the Relative Citation Ratio (RCR). Find more information on RCR.

Example:10,422

Article Type: The article type is based on data from PubMed and preprint servers. For more information, see here.

Example:Meta-analysis

Author Count: This is the total number of authors on the article.

Example:4

Authors: These are the names of all authors as listed on the article. Names may not be full names and may include abbreviations; therefore, use caution when using this field to search or analyze data. Authors are separated by a semi-colon ';'. See more on searching methodologies in the Searching Names tutorial.

Example:”Lelovas, Pavlos P;Xanthos, Theodoros T;Thoma, Sofia E;Lyritis, George P;Dontas, Ismene A”

Authors First Name: This field contains the first names of all authors as listed on the article. If the first name is an initial on the publication only the initial will appear in this field.

Example:“Pavlos;Theodoros;Sofia;George;Ismene”

Author Identifier: Author Identifier is a PubMed field. The author identifier includes a unique identifier associated with an author, corporate or investigator name, if supplied to PubMed by a publisher. The field includes the organization authority that established the unique identifier, such as, ORCID, ISNI, VIAF.

Example:0000-0001-5027-5027-4446

Authors Initials: This field contains the initials of all authors listed on a publication. Authors are separated by a semi-colon ';'. Where an author has a middle initial there is no space between the first and middle initial.

Example:A;VY;IWY;J;CH;DN;TL;ESK;MR;SA

Authors Last Name: This field contains the last names of all authors as listed on the article. This field will reduce false positives if searching using just a last name, e.g., searching Thomas in author name would return authors with a first, middle, or last name of Thomas. Searching the Authors Last Name field would return only last names. See more on how to best search names using the Searching Names tutorial.

Example:“Lelovas;Xanthos;Thoma;Lyritis;Dontas”

Author OPA Person Identifier (OPA ID): Unique identifier for an individual generated by OPA's name disambiguation algorithm.

  Example:df44a4fd22a14184a380f113f07ec4ff

Collective Name: Name of collective group which authored a publication.

  Example:"Asian Institute of Clinical Oncology"

COVID-19 article: This field denotes if a publication or preprint article is considered a COVID-19 article (the focus being the science of COVID-19). Literature with this flag would have been included in the previous OPA iSearch COVID-19 portfolio. The iSearch COVID-19 portfolio was released during the pandemic and was NIH’s comprehensive, expert-curated source for publications and preprints related to either COVID-19 or the novel coronavirus SARS-CoV-2.

Example:Yes

Full Author Affiliation: This field contains the full address and contact details for all authors for publications with fewer than 100 authors. Affiliation may be included for authors, corporate authors, and investigators, e.g., cleveland [ad] AND clinic [ad], if submitted by the publisher. Multiple affiliations were added to citations starting from 2014; previously only the first author’s affiliation was included. PubMed includes the note “Contributed equally” in the affiliation field if this information is supplied by publishers.

Example:“Department of Physiology, University of Texas Health Science Center, San Antonio 78284”

Author location: This is the country or state (if within United States) of the author(s). 

Example:“Hong Kong”

Chemicals and Drugs: These are chemical and drug names extracted from articles using a custom dictionary. The chemicals/drugs dictionary is derived from the MeSH tree.

Example:Estrogen

Cited By Clinical Article: This flag shows whether a publication has been cited by a clinical article. Clinical articles are generally defined as Clinical Trials or Clinical Guidelines. Publication Type flags from PubMed that are used to define clinical articles include: 'Clinical Study', 'Clinical Trial', 'Clinical Trial, Phase I', 'Clinical Trial, Phase II', 'Clinical Trial, Phase III', 'Clinical Trial, Phase IV', 'Adaptive Clinical Trial', 'Controlled Clinical Trial', 'Randomized Controlled Trial', 'Clinical Trial Protocol', 'Observational Study', 'Guideline', and 'Practice Guideline'. See more information on clinical articles.  

In addition, this is a metric used in the publication analysis tool iCite to help measure bench to bedside translation. 

Example:Yes

Cited By PMIDs: For each record this contains the Publication IDs for publications citing the article. Searching this field will return papers which have been cited by your inputted PMID(s).

Example:8633378;1502562;15102042;1456087;9273950;10480411;8833006;19016151;22008303;12908059;11907707;7626314;10459781;16764635;16831929;30847477;7940828;10102557;14672343;19918255;8770690;15206919;15273918;8846757

Cited PMIDs: PMIDs for publications cited by the publication(s) of interest i.e. the reference papers. Searching this field will find all papers that have referenced your inputted PMID(s).

Example:6605973;3752142;3922604;6781728;3503544;6968755;3133194;3500299;6965675;3000756;3492365;3511389;3497347;3508722

Citing Clinical PMIDs: PMIDs that cite PMIDs that have one of these as the Pub Type: 'Clinical Study', 'Clinical Trial', 'Clinical Trial, Phase I', 'Clinical Trial, Phase II', 'Clinical Trial, Phase III', 'Clinical Trial, Phase IV', 'Adaptive Clinical Trial', 'Controlled Clinical Trial', 'Randomized Controlled Trial', 'Clinical Trial Protocol', 'Observational Study', 'Guideline', and 'Practice Guideline'.

   Example:6605973;3752142;3922604

Clinical Article: This is a flag to show whether a publication is defined as a clinical trial or guideline. Publication Type flags from PubMed that are used to define clinical articles include: 'Clinical Trial', 'Clinical Study', 'Clinical Trial, Phase I', 'Clinical Trial, Phase II', 'Clinical Trial, Phase III', 'Clinical Trial, Phase IV' and 'Guideline'. See more information about clinical articles.  

Example:Yes

Condition: Conditions are diseases, disorders, syndromes, illnesses, or injuries that are automatically extracted from publications using natural language processing software that identifies phrases and synonyms along with their associated MeSH semantic type. The conditions dictionary is derived from the MeSH vocabulary tree.

Example:"Alzheimer Disease"

Devices (Extracted): This field uses the article’s title and abstract to return matched terms and phrases from the MeSH dictionary of device terms and phrases. 

Example:Inhaler

DOI: This is a publication or preprint's digital object identifier (doi).

Example:10.1016/b978-0-12-801185-0.00018-0

Expected Citation Rate (ECR): The ECR is calculated using the field citation rate and citation rates for all literature, as part of the Relative Citation Ratio (RCR) calculation. Find more information on RCR.

Example:4.12

Field Citation Rate: This is the average of the journal citation rates for the co-cited articles (includes article of interest). It is calculated as part of the Relative Citation Ratio (RCR) methodology.

Example:9.46

First Author: This is the full name of the first listed author on the publication. See more on how to best search names using the Searching Names tutorial.

Example:“Lelovas, Pavlos P”

Human: This is the percentage of the article’s MeSH terms counted as Human research. This is shown as a score between 0 and 1, with 1 being equivalent to 100%, meaning all terms from the article are Human. See more on this methodology.

Example:0.4

Research Article (iCite Article Type): This flag shows whether a publication is an article type used in iCite. To be counted as an 'article,' a document must have a PubMed "Publication Type" tag indicating a possible research article and no "Publication Type" tags indicating derivative or non-research documents. See more about article types in the iCite user guide.

Example:Yes

ISSN: An ISSN is an 8-digit code used to identify newspapers, journals, magazines and periodicals of all kinds and on all media—print and electronic. The ISSN usually takes the form of the acronym ISSN followed by two groups of four digits, separated by a hyphen. The eighth digit is a check digit calculated according to a modulus 11 algorithm on the basis of the 7 preceding digits; this eighth control digit may be an “X” if the result of the computing is equal to “10" in order to avoid any ambiguity.

Example:0167-6806

Journal Citation Rate: The Journal Citation Rate (JCR) is the citation rate of the journal containing the publication.

Example:3.63

Journal Issue: This is the number of the journal issue in which the article was published.

Example:3

Journal Name: This is the name of the journal that published the publication.

Example:“Nature biotechnology”

Journal Name ISO: This is the abbreviation of the journal name as defined by the International Organization for Standardization. 

Example:“Nat. Biotechnol.”

Journal Pages: This field contains the first and last page numbers of the article in the journal.

Example:497-506

Journal Volume: This is the number of the journal volume in which an article is published.

Example:395

Journal Country: This is the country of the journal that published the publication.

Example:England

Language: This field shows the language in which the article was published. Most languages use the first three letters, except for Japan which is JPN

Example:Chi OR Spa

Last Author: This is the name of the last author on the publication.

Example:“Santangelo, George”

Linked Data: This field shows which other datasets the record is linked to, Grants, Clinical Trials, or Patents. Multiple values are separated by ';'.

   Example:“Clinical Trials”

Linked Clinical Trial Title: Title of the clinical trial(s) linked to the publication. You can search for keywords in the title or the specific title.

  Example:(Tetracaine AND Lidocaine)

Linked Clinical Trial ID: Field contains the clinical trial ID(s) for all clinical trials linked to the publication.

  Example:NCT00827073

Linked Clinical Trial Overall Status: Field contains the overall status of the clinical trial(s) linked to the publication.

  Example:completed

Linked Clinical Trial Start Date: Field contains the start date (actual or planned) for the clinical trial(s) linked to the publication.

  Example:2017-05-20

Linked Clinical Trial Source: Field containing a hyperlink to the clinicaltrials.gov record for the linked clinical trial record. Note this field is not searchable.

Linked Grant Activity Code: NIH and other HHS agencies use letter and number codes, e.g., F32, K08, P01, R01, T32, to differentiate the wide variety of supported programs. Furthermore, individual Activity Codes are also bucketed into larger funding categories, e.g., extramural research (RPG), training, contracts, intramural, and other. See more detail in the Grant Records Search Options/Glossary. This field is available for literature linked to grant records only.

Example:R01

Linked Grant Admin IC: Admin IC represents the full IC acronym, usually 2-5 letters, to designate the agency, NIH Institute, or Center administering the grant. See Institute/Center code definitions. This field is available for literature linked to grant records only.

Example:NHLBI

Linked Grant Fiscal Year: The fiscal year is the annual period established for government accounting purposes and is included for literature linked to grant records only. A fiscal year begins on October 1 and ends September 30 of the following year. Example: FY2018-Started October 1, 2017 and ended September 30, 2018. 

  Example:2017 

Linked Grant Funding Agency: This is the full agency name with acronym for the grant linked to the literature.

Example:“National Institutes of Health”Linked Grant Number: Grant number linked to a publication.

  Example:R01GM148970

Linked Grant PIIDs: PI IDs of principal investigators (PIs) with grants linked to a publication. 

  Example:1881423

Linked Grant PI Names: Names of principal investigators with grants linked to a publication. 

  Example:"John Morrison"

Linked Grant Link Type: Field containing the link type (SPIRES or Disambiguation). See more about this methodology in the linked data article.

  Example:SPIRES;disambiguation

Linked Grant Source: Field containing a hyperlink to the RePORTER record for the linked grant. Note this field is not searchable.

  Example:https://reporter.nih.gov/project-details/2838343

Linked Grants Count (Count of Linked Grants): The total number of grants linked to the article.

  Example:5

Linked Patent/Associated Patent Assignees: The assignees is the entity that is the recipient of a transfer of a patent application, patent, trademark application or trademark registration from its owner of record (assignor). This field exists for patents linked to literature

Example:"New York University"

Linked Patent/Associated Patent Filing date: The date of receipt in the Office of an application which includes (1) a specification containing a description and, if the application is a nonprovisional application, at least one claim, and (2) any required drawings. This field exists for patents linked to literature

Example:2017-05-20

Linked Patent/Associated Patent Inventors: A person who contributes to the conception of an invention. The patent law of the United States of America requires that the applicant in a patent application must be the inventor. This field exists for patents linked to literature

Example:"rossi, john j"

Linked Patent/Associated Patent Number/Patent ID: This is a linked data filter that identifies Literature cited by patents via the Non-Patent Citation field in USPTO data. A citation resolution algorithm resolves a free-text citation to a PMID for the linking. Multiple values are separated by ';'.

Example:US-9982277-B2

Linked Patent/Associated Patent Publication Date: Publication date of the linked patent.

Example:2017-05-20

Linked Patent/Associated Patent Title: This field contains the title text from the patent linked to the literature. You can search for keywords in the title or the specific title.

  Example:cancer

Linked Patent/Associated Patent Type: Field to indicate whether the linked patent record is an ‘Application’ or ‘Granted’ patent.

Example:Granted

MeSH Keywords: The Medical Subject Headings (MeSH) thesaurus is a controlled and hierarchically organized vocabulary produced by the National Library of Medicine (NLM). MeSH keywords are tagged onto articles based on content in the Title and Abstracts. Learn more about the NLM process.

Example:“CRISPR-Cas Systems”

MeSH Plus: The Medical Subject Headings (MeSH) thesaurus is a controlled and hierarchically organized vocabulary produced by the National Library of Medicine (NLM). MeSH plus terms are extracted from the Title, Abstract, (PubMed) MeSH, and (PubMed) keywords using synonyms. This field will capture broader results compared to MeSH Keywords. Learn more about the NLM process.

Example:“CRISPR-Cas Systems”

Molecular/Cellular: This is the percentage of the article’s MeSH terms counted as Molecular/Cellular research. This is shown as a score between 0 and 1, with 1 being equivalent to 100%, meaning all terms from the article are Molecular/Cellular. See more on this methodology in the iCite user guide.

Example:0.2

NIH Linked: Indicates whether a publication is linked to an NIH grant. This field is used in the topic explorer visualization heat mapping.

Example:Yes

NIH RCR Percentile: Value from 0 (lowest) to 100 (highest) showing where the publications RCR value falls within the distribution for NIH funded publications.

Example:95

NLM Unique ID: This is a unique alphanumeric identifier for the journal that was assigned by the NLM Integrated Library System Locator Plus.

Example:0375267

PubMed Keywords: These are keywords provided by the publisher. This field is also known as Other Term in MEDLINE.

Example:Progesterone

PMCID: This is a unique number assigned to a work that is posted to PubMed Central (PMC), a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH) developed and managed by NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM). All works applicable under the NIH Public Access Policy are posted to PubMed Central.

  Example:PMC7228350

PMID: PMID is the unique identifier number used in PubMed. The PMID# is always found at the end of a PubMed citation. In addition, some preprints will also have a PMID as PubMed has been including preprints in recent years. PMIDs for the preprints will appear under Alt ID in iSearch Analytics but will not be the main identifier. 

Example:25398350

Posted Date: This is the publication date of an article or the posted date of a preprint article.

Example:2014-01-01

Preprint: This flag identifies if an article is a preprint. Preprint articles are complete and/or public drafts of scientific documents. Preprints may be peer reviewed but do not follow the same procedures as peer-reviewed journal articles. These documents are significant as they ensure new research is disseminated into the scientific community to invite feedback, improve work, and establish priorities on rapidly developing topics, such as COVID-19. Read more about preprints. (Note that iSearch includes preprints from the PubMed preprint pilot and directly from a number of other preprints servers as well.)

Example:Yes

Published As: This shows the later DOI where are preprint has a later version, either a newer preprint, or a peer reviewed publication. The later version may or may not have a PMID/be in PubMed.

Example:10.1186/s13063-019-3235-5

RCR is Provisional: RCRs for papers published in the previous two years are flagged as "provisional," to reflect that citation metrics for newer articles are not necessarily as stable as they are for older articles. See the defining iSearch data page in the FAQs section of the user guide for more details. Values are Yes or blank. Learn more about provisional RCRs. 

Example:No

Relative Citation Ratio (RCR): Provides the Relative Citation Ratio (RCR) for all Literature where an RCR is available. RCR is a citation-based measure of scientific influence.  It is calculated as the citations a publication receives per year, normalized to citations received by NIH-funded papers published in the same year and field. The median RCR for NIH-funded papers is 1. Therefore, an RCR over 1 indicates more citations/influence than average, whereas an RCR under 1 indicates fewer citations/less influence. Learn more about RCR and how to compare RCR values for non-NIH funded papers. RCR is potentially available for any publication linked to a grant record. More RCR metrics and visualizations can be seen in our public publication analysis tool, iCite. 

Example:2.0

Source: The source of the article, e.g. PubMed or a preprint server.

Example:PubMed

Substances: Articles are tagged with chemical and substance keywords from the National Library of Medicine (NLM). The source for these is PubMed or, specifically, PubChem. Keywords can contain chemical structures, synonyms, registration IDs, descriptions, related URLs, patent identifiers, cross-references to PubMed, biological screening results, etc. See more on PubChem substances.

Example:RNA

System ID: This is the unique ID for each record within iSearch. For literature, it will be the PMID if the source is PubMed or the doi if the source is a preprint server.

Example:32007143

To further compare the IDs in Literature, see the examples below:

Target: These are drug targets and are created using a dictionary of target terms and searching the text of the Title and/or Abstract in Literature. The dictionary comes from the IUPHAR/BPS Guide to Pharmacology. 

Example:SLC12A9

Title: This is the full title of the article. If using this as a search field, you can find terms or phrases in the title without having to include the entire, exact title.

Example:Tumorigenesis

Total Citations: This is the total number of publications citing the article.

Example:3

Total Clinical Citations: This is the total number of clinical citations that the article has. See Citing Clinical PMIDs for more details.

Example:3

Total Clinical Trials: This is the total number of clinical trials linked to the article.

Example:3

Total Patents: This is the total number of patents linked to the article.

Example:3

Total References: This is the total number of papers cited by the article of interest.

Example:15

Year: The year of publication of the article of interest.

Example:2017