ADDING MACHINE-READABLE BIBLIOGRAPHIC METADATA TO SCHOLARLY ARTICLES Section 1: Overall guidelines Section 2: List of metatags Section 3: Abstract markup Section 4: Structured references Section 5: Unstructured references We use HTML metatags to embed machine-readable bibliographic metadata within all HTML versions of scholarly articles (abstracts as well as fulltext). In addition, we provide a mechanism to associate the metadata with the fulltext PDF version of the article. Section 1: Overall guidelines The section below includes basic information on field formatting, character escaping, encoding, etc. that are essential to ensuring bibliographic data within the metatags are represented as accurately as possible within indexing systems. Encoding: please use the same character encoding (eg UTF-8, ISO-8859-1, etc) for metatags as you are using for the HTML page text. Escaping: as per HTML standards, angle brackets (< and >) and ampersand (&) MUST be escaped in metatag values. Standard HTML entities (ie, < > and &) work well for this purpose. Furthermore, the character used to delimit the value field of the metatag would MUST be escaped. As an example, for an article titled "'Who shall see the wind?' A Study in Contrasts", the metatag would be: Missing fields: Skip/drop all missing fields. Please don't use placeholder values. Order of fields: There are two ordering constraints. First, authors MUST be listed in the same order as they are in the article. Second, all information for a single author MUST be grouped together and the author s name MUST come before all other information for the author.. There are no other ordering constraints. Section 2: List of metatags This is the list of all the metatags used to specify bibliographic metadata - for article metadata as well as for references. Note that some of the fields are available only in article metadata. Unless explicitly specified as repeatable, each field MUST occur at most once. 1
Full name of the journal: This field should include the full name of the journal and NOT an abbreviation. Abbreviated name for the journal : This field contains the journal-name abbreviation and can be repeated. Examples: Publisher name: This should be the formal publisher of the journal/book chapter, and not the software platform or hosting service. Author information: These fields correspond to a single author. Information for a single author MUST occur as a group. The first field in the group MUST be citation_author. The other fields are optional and can occur in any order. Authors MUST be listed in the same order as in the article itself. 2
Common problems with author names: Title of the item: This field corresponds to the title of the publication and includes complete subtitles. For journal articles, conference articles, preprints, technical reports, working papers, use for the title of the article. For complete books (i.e. not chapters), use this tag for the title of the entire book. For book chapters, use for the title of the chapter and citation_inbook_title for the title of the entire book (more on citation_inbook_title below). Journal title example: Additional example, with a subtitle: Title for chapters in an edited volume: If the item is a chapter in an edited volume. 3
For example: NOTE: The "citation_inbook_title" field is ONLY for chapters in edited volumes. In particular, it is NOT meant for the title of the monograph. Common problems with titles for edited volumes and their chapters: Publication date: This is the date that the item is published. For journal articles, this is the ISSUE or the COVER date. This is NOT the date the article first become available online (for that, see citation_online_date below). Format of the date MUST be YYYY/MM/DD, YYYY/MM or YYYY. Please use the format that best fits the publication date for the article. If the issue date is May 24, 2004, the tag would be: If the issue date is just May 2004 (without a day), the tag would be: Online availability date: this is the date the article became available online. Format of the date MUST be YYYY/MM/DD. For ahead-of-print articles, this is the date the article became available online. At least one of OR citation_online_date MUST be included. It is ok to include both. 4
Example of an online-publication date: Example of the final and online dates grouped together: Journal volume: For journal articles, this is the volume the article is published in. Journal issue: For journal articles, this is the issue the article is published in. NOTE: For ahead-of-print articles that have not been assigned to a specific volume or issue, please leave citation_volume and citation_issue out. Page numbers: First and last page for the article. For online-only articles which don't have page numbers, but have an article-number or an elocation-id, please use citation_firstpage for the article-number or elocation-id and skip citation_lastpage, e.g. If it is not possible to separate first page and last page, please include the page range using a citation_pages metatag, e.g. DOI: Please include ONLY the DOI itself, and NOT the dx.doi.org URL. 5
Free-to-read marker: This is a boolean marker to indicate that the article is free-to-read for all users. Note that this marker is intended for articles that are permanently free-to-read. This MUST NOT be used for articles that are free-to-read to all users only for a short period. The value of this metatag MUST be empty - it is a boolean marker with no additional specification. Metatags with a non-empty value will be ignored. Fulltext PDF URL: the URL MUST be on the same host as the abstract/full-text html. For example, if abstracts for a journal are hosted on www.example-journal.org, the corresponding PDFs should also be hosted on www.example-journal.org. If the papers were located on a different host, e.g. papers.example-journal.org, then the system could not associate the abstract and metadata with the fulltext document. Journal ISSN: please include all ISSNs. This field can be repeated. Example, including both print and electronic ISSNs: Arxiv ID: This should be included only for articles in the arxiv repository (arxiv.org). PubMed ID: This should be included only for articles in the PubMed collection of abstracts. Article language: This is the language the article itself is written in. even if the abstract text is in a different language. 6
Article type: This is the article type, e.g. "Research Article", "Review Article", "Case Report", "Editorial", etc. Keywords: keywords and keyphrases. Please use semicolons to separate keywords/keyphrases. This field can be repeated. Conference title: For conference articles, the full, unabbreviated name of the conference. Example : Conference abbreviation: This field contains the abbreviation of the conference title. Multiple abbreviations are okay, one field per abbreviation. Example : 7
Conference series ID: If the paper is a conference article, the value of this tag includes the publisher prefix, followed by the conference series ID, which is a unique ID for the conference. This ID may not appear in a formal citation (or anywhere else in search results). Example : Conference sequence number: This field contains the conference sequence number. ISBN: If the item is a monograph. DO NOT include if the item is a chapter in an edited book volume. Funding source: All information about one funding award is contained in a single metatag. Each funding award should be in its own metatag. This field can be repeated. The name of the metatag is citation_funding_source and the value is constructed by joining individual subfield-value pairs separated by semi-colons. The subfields for a funding source are: citation_funder: This is the name of funder. An example would be "National Science Foundation". This subfield is REQUIRED. citation_funder_id: This is the CrossRef funder identifier. This subfield is OPTIONAL. ciitation_grant_number: This is the number or identifier of the funding grant. This subfield is OPTIONAL. This subfield is highly recommended and should be included when available. 8
citation_grant_recipient: This is name of the funded researcher. This subfield can be repeated. Please use a separate subfield for each name. This subfield is OPTIONAL. This subfield is highly recommended and should be included when available. Here is a quick example to illustrate the structure. Funding information: This research was funded by T32 DK07634 and K24DK100548 from the National Institutes of Health. Funding support from Q10 Covidien Medical was received by R. Rothstein, A. Infantolino, A. Ertan. Metatag representation: Patent information: Include these fields if the item is a patent. Note that it's okay to include multiple tags if patent is valid in multiple countries. ISO 3166-1 alpha-3 codes can be found at http://en.wikipedia.org/wiki/iso-3166-1_alpha-3. Technical report information: Tags to include if item is a technical report. Dissertation institution: If the item is a dissertation or thesis. 9
Section 3: Abstract markup This section describes how to markup abstracts for improved indexing and discoverability of abstract text in search results. To markup abstracts for indexing, an article MUST include the machine- readable bibliographic information via HTML metatags, as specified above. In addition, the abstract for the article MUST be viewable by all users. Finally, the complete abstract MUST be specified using a citation_abstract metatag. There are four issues to keep in mind when marking up abstracts for indexing: (1) Some abstracts are structured and contain subsections. Use <h3>, <p>, <b> and <i> to format the abstract including paragraphs and headings. See example 1 below. (2) Some abstracts contain superscripts/subscripts or emphasized phrases/terms. Use <sup> and <sub> to specify superscripts & subscripts. Use <b> and <i> to indicate emphasized phrases/terms. See example 2 below. (3) Some abstracts include mathematical equations and formulas which can't be directly described in HTML. For mathematical equations and formulas that occur in abstracts, use LaTeX formatting as described in MathJax Tex and LaTex Support. See example 3 below. (4) If the abstract appears in multiple languages, include all versions of the abstract. Use a separate metatag for each language version. Use the lang attribute of the metatag to specify the language of the abstract. Use the ISO 639-1 language code for the language. See example 4 below. To ensure that the abstract metatags are valid HTML, HTML-escape the metatags' content attribute by replacing '<' with <, '>' Example 1: Section headers Background Clear, transparent, and sufficiently detailed abstracts of conferences and journal articles related to randomized controlled trials (RCTs)are important, because readers often base their assessment of a trial solely on information in the abstract. Here, we extend the CONSORT (Consolidated Standards of Reporting Trials) Statement to develop a minimum list of essential items, which authors should consider when reporting the results of a RCT in any journal or conference abstract. Methods and Findings We generated a list of items from existing quality assessment tools and empirical evidence. A three-round, modified-delphi process was used to select items. In all, 109 participants were invited to participate in an electronic survey; the response rate was 61%. Survey results were presented at a meeting of the CONSORT Group in Montebello, Canada, January 2007, involving 26 participants, including clinical trialists, statisticians, epidemiologists, and biomedical editors. Checklist items were discussed for eligibility into the final checklist. The checklist was then revised to ensure that it reflected discussions held during and subsequent to the 10
meeting. CONSORT for Abstracts recommends that abstracts relating to RCTs have a structured format. Items should include details of trial objectives; trial design (e.g., method of allocation, blinding/masking); trial participants (i.e. description, numbers randomized, and number analyzed); interventions intended for each randomized group and their impact on primary efficacy outcomes and harms; trial conclusions; trial registration name and number; and source of funding. We recommend the checklist be used in conjunction with this explanatory document, which includes examples of good reporting, rationale, and evidence, when available, for the inclusion of each item. Conclusions CONSORT for Abstracts aims to improve reporting of abstracts of RCTs published in journal articles and conference proceedings. It will help authors of abstracts of these trials provide the detail and clarity needed by readers wishing to assess a trial's validity and the applicability of its results. Marked up abstract: Example 2: Abstract with Italics We have have adapted a bacterial CRISPR RNA/Cas9 system to precisely engineer the Drosophila genome and report that Cas9-mediated genomic modifications are efficiently transmitted through the germline. This RNA-guided Cas9 system can be rapidly programmed to generated targeted alleles for probing gene function in Drosophila. Marked up abstract: 11
Section 4: Structured references Each reference is contained in a single metatag. The name of the metatag is citation_reference. The value of a reference metatag is constructed by joining individual field-value pairs separated by semi-colons. The names of the fields, their formatting and order constraints and their semantics are the same as those used for article metadata. A quick example to illustrate the structure is as follows: Reference: A. Einstein, B. Podolsky; N. Rosen, "Can quantum-mechanical description of physical reality be considered complete?", Physical Review 47(10) pp 777-780, 1935 Metatag representation: We provide a list of commonly used fields for different kinds of references (journal articles, books, book chapters, technical reports, preprints, dissertations etc.) below. For each item type, we have included an example metatag representation. Journal article: citation_journal_title citation_author (one author per field) citation_volume citation_issue citation_firstpage citation_lastpage citation_issn citation_doi Book: citation_author (one author per field) citation_publisher citation_isbn 12
Book chapter: (chapter title) citation_inbook_title (title of the book) citation_author (one author per field) citation_publisher citation_firstpage citation_lastpage Conference article: citation_conference_title (full name of the conference) citation_author (one author per field) citation_firstpage citation_lastpage Dissertation: citation_author (there should be only one author for a dissertation) citation_dissertation_institution 13
Arxiv preprint: citation_author (one author per field) citation_arxiv_id Other technical report or preprint: citation_author (one author per field) citation_technical_report_institution citation_technical_report_number Patent: citation_author (one author/inventor per field) citation_patent_number citation_patent_country Non-classifiable: citation_author (one author per field) citation_publisher Section 5: Unstructured references WARNING : Adding unstructured references to article pages is intended to be used ONLY if there is absolutely no other option. Depending on how things are laid out, and how widely this 14
approach is used, it can result in a substantial fraction of references to be dropped from indexing. The recommended and the likely-to-work-well approach is outlined above in Section 3. This is a fallback approach for references. It is intended for references that are not or cannot be partitioned into individual fields. The idea here is simple: Just include the entire reference as the value of the citation_reference metatag. Wherever possible, please include structured references as it would help ensure effective indexing. If detailed field information available for some of the references but not for others, we recommend using the structured format for the references with detailed information is available and the unstructured format for the remaining few for which detailed field information is not available. A. Einstein, B. Podolsky; N. Rosen, "Can quantum-mechanical description of physical reality be considered complete?", Physical Review 47(10) pp 777-780, 1935 would be represented as: 15