Overview
The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary reference, then there is no JRNL reference. Other references are given in REMARK 1.
PDB is in the process of linking and/or adding all references to CitDB, the literature database used by the Genome Data Base (available at URL http://gdbwww.gdb.org/gdb-bin/genera/genera/citation/Citation).
Record Format
COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 70 LString text See Details below.
Details
* The following tables are used to describe the sub-record types of the JRNL record.
* The AUTH sub-record is mandatory in JRNL. This is followed by TITL, EDIT, REF, PUBL, and REFN sub-record types. REF and REFN are also mandatory in JRNL. EDIT and PUBL may appear only if the reference is to a non-journal.
* If the JRNL reference is in the MEDLINE database the information in the MEDLINE reference will be used to supply information for the sub-record types.
* When a MEDLINE reference is used, the abbreviation of the journal will be converted to the CASSI abbreviation as listed in the coden list used jointly by the Cambridge Crystallographic Data Centre (CCDC) and the PDB.
1. AUTH
* AUTH contains the list of authors associated with the cited article or contribution to a larger work (i.e., AUTH is not used for the editor of a book).
* The author list is formatted similarly to the AUTHOR record. It is a comma-separated list of names. Spaces at the end of a sub-record are not significant; all other spaces are significant. See the AUTHOR record for full details.
* The authorList field of continuation sub-records in JRNL differs from that in AUTHOR by leaving no leading blank in column 20 of any continuation lines.
* One author's name, consisting of the initials and family name, cannot be split across two lines. If there are continuation sub-records, then all but the last sub-record must end in a comma.
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 16 LString(4) "AUTH" Appears on all continuation records.
17 - 18 Continuation continuation Allows concatenation of multiple
records.
20 - 70 List authorList List of the authors.
2. TITL
* TITL specifies the title of the reference. This is used for the title of a journal article, chapter, or part of a book. The TITL line is omitted if the author(s) listed in authorList wrote the entire book (or other work) listed in REF and no section of the book is being cited.
* If an article is in a language other than English and is printed with an alternate title in English, the English language title is given, followed by a space and then the name of the language (in its English form, in square brackets) in which the article is written.
* If the title of an article is in a non-Roman alphabet the title is transliterated.
* The actual title cited is reconstructed in a manner identical to other continued records, i.e., trailing blanks are discarded and the continuation line is concatenated with a space inserted.
* A line cannot end with a hyphen. A compound term (two elements connected by a hyphen) or chemical names which include a hyphen must appear on a single line, unless they are too long to fit on one line, in which case the split is made at a normally-occurring hyphen. An individual word cannot be hyphenated at the end of a line and put on two lines. An exception is when there is a repeating compound term where the second element is omitted, e.g., "DOUBLE- AND TRIPLE-RESONANCE". In such a case the non-completed word "DOUBLE-" could end a line and not alter reconstruction of the title.
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "TITL" Appears on all continuation lines. 17 - 18 Continuation continuation Permits long titles. 20 - 70 LString title Title of the article.
3. EDIT
* EDIT appears if editors are associated with a non-journal reference. The editor list is formatted and concatenated in the same way that author lists are.
COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(4) "EDIT" Appears on all continuation records. 17 - 18 Continuation continuation Allows a long list of editors. 20 - 70 List editorList List of the editors.
4. REF
* REF is a group of fields which contains either the publication status or the name of the publication (and any supplement and/or report information), volume, page, and year. There are two forms of this sub-record group, depending upon the citation's publication status.
4a. If the reference hasnot yet been published, the sub-record type group has the form:
COLUMNS DATA TYPE FIELD DEFINITION -------------------------------------------------------------------------------- 1 - 6 Record name "JRNL " 13 - 16 LString(3) "REF" 20 - 34 LString(15) "TO BE PUBLISHED"
* At the present time, there is no formal mechanism in place for monitoring the subsequent publication of such referenced papers. PDB relies upon the depositor to provide reference update information since preliminary information can change by the time of actual publication.
4b. If the reference has beenpublished, then the REF sub-record type contains information about the name of the publication, supplement, report, volume, page, and year in the appropriate fields. These fields are detailed below.
* Publication name (first item in pubName field):
- If the publication is a serial (i.e., a journal, an annual, or other non-book or non-monographic item issued in parts and intended to be continued indefinitely), use the abbreviated name of the publication as listed in American Chemical Society (A.C.S.) publications such as CAS Source Index (CASSI) or Chemical Abstracts. (The A.C.S. abbreviation is based on the International Standards Organization's standard ISO 4-1984[E].) If the A.C.S. has not yet established an abbreviation for the publication, the name is given in full.
- If the publication is a book, monograph, or other non-serial item, use its full name according to the Anglo-American Cataloging Rules, 2nd Ed., 1988 revision (AACR2R). (Non-serial items include theses, videos, computer programs, and anything that is complete in one or a finite number of parts.) If there is a sub-title, and the item is verified in an online catalog, it will be included using the same punctuation as in the source of verification. Preference will be given to verification using cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.
- If a book is part of a monographic series: the full name of the book (according to AACR2R) is listed first, followed by the name of the series in which it was published. The series information is given within parentheses and the series name is preceded by "IN:" and a space. If the series has an A.C.S. abbreviation, that abbreviation should be used; otherwise the series name should be listed in full. If applicable, the series name should be followed, after a comma and a space, by a volume (V.) and/or number (NO.) and/or part (PT.) indicator and the relevant characters to indicate its number and/or letter in the series.
* Supplement (follows publication name in pubName field):
- If a reference is in a supplement to the volume listed, or if information about a "part" is needed to distinguish multiple parts with the same page numbering, such information should be put in the REF sub-record.
- A supplement indication should follow the name of the publication and should be preceded by a comma and a space. Supplement should be abbreviated as "SUPPL." If there is a supplement number or letter, it should follow "SUPPL." without an intervening space. A part indication should also follow the name of the publication and be preceded by a comma and a space. A part should be abbreviated as "PT.", and the number or letter should follow without an intervening space.
- If there is both a supplement and a part, their order should reflect the order printed on the work itself.
* Report (follows publication name and any supplement or part information in pubName field):
- If a book has a report designation, the report information should follow the title and precede series information. The name and number of the report is given in parentheses, and the name is preceded by "REPORT:" and a space.
* Reconstruction of publication name:
- The name of the publication is reconstructed by removing any trailing blanks in the pubName field, and concatenating all of the pubName fields from the continuation lines with an intervening space. There are two conditions where no intervening space is added between lines: when the pubName field on a line ends with a hyphen or a period, or when the line ends with a hyphen (-). When the line ends with a period (.), add a space if this is the only period in the entire pubName field; do not add a space if there are two or more periods throughout the pubName field, excluding any periods after the designations "SUPPL", "V", "NO", or "PT".
* Volume, page, and year (volume, page, year fields respectively):
- The REF sub-record type group also contains information about volume, page, and year when applicable.
- In the case of a monograph with multiple volumes which is also in a numbered series, the number in the volume field represents the volume number of the book, not the series. (The volume number of the series is in parentheses with the name of the series, as described above under publication name.)
COLUMNS DATA TYPE FIELD DEFINITION
--------------------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 16 LString(3) "REF"
17 - 18 Continuation continuation Allows long publication names.
20 - 47 LString pubName Name of the publication including
section or series designation. This is
the only field of this sub-record which
may be continued on successive
sub-records.
50 - 51 LString(2) "V." Appears in the first sub-record only,
and only if column 55 is non-blank.
52 - 55 String volume Right-justified blank-filled volume
information; appears in the first
sub-record only.
57 - 61 String page First page of the article; appears in the
first sub-record only.
63 - 66 Integer year Year of publication; first sub-record
only.
5. PUBL
* PUBL contains the name of the publisher and place of publication if the reference is to a book or other non-journal publication. If the non-journal has not yet been published or released, this sub-record is absent.
* The place of publication is listed first, followed by a space, a colon, another space, and then the name of the publisher/issuer. This arrangement is based on the ISBD(M) International Standard Bibliographic Description for Monographic Publications (Rev.Ed., 1987) and AACR2R and is used in public online catalogs in libraries. Details on the contents of PUBL are given below.
* Place of publication:
- Give the place of publication. If the name of the country, state, province, etc. is considered necessary to distinguish the place of publication from others of the same name, or for identification, then follow the city with a comma, a space, and the name of the larger geographic area.
- If there is more than one place of publication, only the first listed will be used. If an online catalog record is used to verify the item, the first place listed there will be used, omitting any brackets. Preference will be given to the cataloging done by the Library of Congress, the National Library of Medicine, and the British Library, in that order.
* Publisher's name (or name of other issuing entity):
- Give the name of the publisher in the shortest form in which it can be understood and identified internationally, according to AACR2R rule 1.4D.
- If there is more than one publisher listed in the publication, only the first will be used in the PDB file. If an online catalog record is used to verify the item, the first place listed there will be used for the name of the publisher. Preference will be given to the cataloging of the Library of Congress, the National Library of Medicine, and the British Library, in that order.
* Ph.D. and other theses:
- Theses are presented in the PUBL record if the degree has been granted and the thesis made available for public consultation by the degree-granting institution.
- The name of the degree-granting institution (the issuing agency) is followed by a space and "(THESIS)".
* Reconstruction of place and publisher:
- The PUBL sub-record type can be reconstructed by removing all trailing blanks in the pub field and concatenating all of the pub fields from the continuation lines with an intervening space. Continued lines do not begin with a space.
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 16 LString(4) "PUBL"
17 - 18 Continuation continuation Allows long publisher and place names.
20 - 70 LString pub City of publication and name of the
publisher/institution.
6. REFN
* REFN is a group of fields which contains encoded references to the citation. No continuation lines are possible. Each piece of coded information has a designated field.
* The American Society for Testing and Materials (ASTM) number is an encoded reference to the journal title. New ASTM codens are assigned by the Chemical Abstracts Service and appear in CASSI and its supplements.
* The country field is blank if the reference was published in more than one country.
* If more than one ISBN is known, select one that matches the individual volume cited (if it happens to be in a set that also has an ISBN for the set). If the reason for multiple ISBNs is that the publication is issued in more than one country, use the ISBN for the country of the first listed place of publication. If there are hardcover and paperback ISBN numbers, use the ISBN for the hardbound version.
* Because some publications do not have an ASTM coden, an ISSN number, or an ISBN number, each publication is assigned a number. This list of numbers, or codens, was established by the Cambridge Crystallographic Data Center (CCDC) and new numbers are assigned by both CCDC and PDB as new publications are added to their respective databases.
* There are two forms of this sub-record type group, depending upon the publication status.
6a. This form of the REFN sub-record type group is used if the citation has not been published.
COLUMNS DATA TYPE FIELD DEFINITION
--------------------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 16 LString(4) "REFN"
67 - 70 LString(4) "0353" This is the CCDC/PDB coden for unpublished
works.
6b. This form of the REFN sub-record type group is used if the citation has been published.
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 16 LString(4) "REFN"
20 - 23 LString(4) "ASTM"
25 - 30 LString(6) astm ASTM devised coden.
33 - 34 LString(2) country Country of publication code as defined
in the OCLC/MARC cataloging format
(optional).
36 - 39 LString(4) "ISBN" or International Standard Book Number or
"ISSN" International Standard Serial Number.
41 - 65 LString isbn ISSN or ISBN number (final digit may be
a letter and may contain one or more
dashes).
67 - 70 LString(4) coden Code from CCDC/PDB coden list.
Verification/Validation/Value Authority Control
PDB verifies that this record is correctly formatted.
PDB uses MEDLINE to verify the accuracy of references and to obtain information required for CitDB that is not required by the PDB listing. The process of using MEDLINE requires following the National Library of Medicine rules for the transcription of names and titles. Articles in non-MEDLINE journals are verified through other online databases or with the reprint in hand. Verification of book references is done using online cooperative or individual library catalogs.
Citations appearing in JRNL may not also appear in REMARK 1.
Relationships to Other Record Types
The publication cited as the JRNL record may not be repeated in REMARK 1.
Example
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
JRNL AUTH N.THANKI,J.K.M.RAO,S.I.FOUNDLING,W.J.HOWE,
JRNL AUTH 2 A.G.TOMASSELLI,R.L.HEINRIKSON,S.THAISRIVONGS,
JRNL AUTH 3 A.WLODAWER
JRNL TITL CRYSTAL STRUCTURE OF A COMPLEX OF HIV-1 PROTEASE
JRNL TITL 2 WITH A DIHYDROETHYLENE-CONTAINING INHIBITOR:
JRNL TITL 3 COMPARISONS WITH MOLECULAR MODELING
JRNL REF TO BE PUBLISHED
JRNL REFN 0353
JRNL AUTH G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME
JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT
JRNL TITL 2 1.74 A RESOLUTION
JRNL REF J.MOL.BIOL. V. 175 159 1984
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070
Known Problems
* Interchange of bibliographic information and linking with other databases is hampered by the lack of labels or specific locations for certain types of information or by more than one type of information being in a particular location. This is most likely to occur with books, series, and reports. Some of the points below provide details about the variations and/or blending of information.
* Titles of the publications that require more than 28 characters on the REF line must be continued on subsequent lines. There is some awkwardness due to volume, page, and year appearing on the first REF line, thereby splitting up the title.
* Information about a supplement and its number/letter is presented in the publication's title field (on the REF lines in columns 20 - 47). This sometimes means that the publication's coden has several versions of REF title information.
* When series information for a book is presented, it is added to the REF line. The number of REF lines can become large in some cases because of the 28-column limit for title information in REF.
* There is often an ISBN for a book title and a separate ISSN for the series in which it was published. There is no way to present more than one of these.
* Books that are issued in more than one series are not accommodated.
* Many books are issued in more than one country. The publisher has a separate ISBN number in each country. There is no place to put any additional applicable ISBN numbers, which would be useful in an international database such as the PDB.
* The country code prefix of the ISBN may not match the country of the place of publication that is listed on the PUBL line when a book is published in more than one country.
* Pagination is limited to the beginning page.
* There is no place for listing a reference's accession number in another database.
* MEDLINE truncates the author list after the tenth name.