Difference between revisions of "FlyBase:Reference Report"

Revision as of 10:52, 12 December 2017

The Reference Report includes the bibliographic citation, abstract, external IDs (PubMed, PubMed Central, DOI), and links to other FlyBase Report pages for any objects curated from the reference.

Reference

This section provides the key bibliographic details about the reference.

Header	Clicking on the 'Download as RIS’ icon at the end of the header line downloads a tagged text file of citation data that can be imported into any standard reference manager.
Citation	The exact content of this field differs by publication type but, where applicable, the information is in the following order: authors (surname. initials), year, title, journal abbreviation, volume, issue number, page range/article number/URL. Where available, the citation includes a hyperlink to the relevant webpage on the journal's website.
FlyBase ID	The unique FlyBase identifier for the reference (FBrf).
Publication Type	Term from the the publication class section of the FlyBase Controlled Vocabulary.
Abstract	The abstract of the reference, usually obtained from PubMed.
PubMed ID	The PubMed identification (PMID) number for the reference, where available, hyperlinked to the relevant page at PubMed.
PubMed Central ID	The PubMed Central identification (PMCID) number for the reference, where available. Hyperlinks are provided both for NCBI PubMed Central and Europe PubMed Central.
DOI	The Digital Object Identifier for the reference, if available, hyperlinked to the relevant webpage on the journal's website.
ISBN	The 'International Standard Book Number' (ISBN) for references of the publication type 'book'. This field is only present if it has content.
Text of Personal Communication	The text of a 'personal communication to FlyBase', if available. If unavailable, the message 'Paper copy archived' will be shown and users can contact FlyBase for a copy. This field is only present if it has content. Any files that accompany the personal communication will be displayed in the Associated Information section below.

Related Publication(s)

This section lists any references in FlyBase that are directly linked to the current Reference Report. Common examples of relationship types are:

a research paper and an erratum
a research paper and a commentary
a research paper and a personal communication to FlyBase
a research paper and its supplementary material
distinct publications (e.g. a different languages and/or in a different journals) of the same paper in different formats (e.g. FBrf0194405)

Instances of the last example are displayed in a separate subsection titled 'Also Published As'.

The publication type of the related reference is given in the left-hand column and the citation of that reference is provided in the right-hand column, with its FlyBase ID hyperlinked to the corresponding Reference Report.

Recent Updates

This section lists objects (e.g., genes, alleles, transgenic constructs) that were associated with the reference in each FlyBase release. It currently only tracks new links and not links that were removed.

Associated Information

Comments	Used by FlyBase curators to provide comments about the content of a reference. This field is blank in most cases, but is often filled in for references of the type 'FlyBase analysis'.
Associated Files	The names of, and links to, any files that accompany the given reference (usually a 'personal communication to FlyBase') but are not in text format and so cannot be displayed in situ (e.g. spreadsheets, images). Entries have the format "File date; File size; File format; File name".

Other Information

Secondary IDs	Any secondary FlyBase identifier (FBrf) number(s) used previously for the given reference. If present, this generally indicates that duplicate reference entries have been merged in the database.
Language of Publication	The language in which the main text (i.e. the non-abstract sections) of the publication is written.
Additional Languages of Abstract	Where the abstract of a publication is provided in more than one language (even when the main text of the paper is in a single language), it is listed here.

Parent Publication

Most references in FlyBase are not stand-alone publications, but are published within a 'parent publication' - usually a journal or sometimes an edited book. Details of the parent publication are given in this section.

Publication Type	Either 'journal', 'book', or the catch-all term 'compendium', taken from the publication class section of the FlyBase Controlled Vocabulary.
Abbreviation	The FlyBase abbreviation for the parent publication. Journal abbreviations usually mirror those used at PubMed.
Title	The full title of the parent publication.
Editors	The editor(s) where the parent publication is an edited book. Names are listed in the format "surname. initials". This field is only present if it has content.
Publication Year	The year in which an edited book was published, or the years of publication of a journal (only shown for older journals). This field is only present if it has content.
ISBN/ISSN	The International Standard Book Number (ISBN) where the parent publication is an edited book, or one or more International Standard Serial Numbers (ISSN) where the parent publication is a journal.

Data from Reference

This section provides a list of database objects (genes, alleles, aberrations, transgenic constructs etc.) that have been curated from the reference, each hyperlinked to their respective Report page. Objects are organized into subsections according to type and presented in alphabetical order. Subsections are only present where relevant data has been curated, meaning that this entire section will be blank for uncurated references, or will only have a 'Genes' subsection if that is the only object type curated.

@@ Line 1: / Line 1: @@
-Last Updated: October 2012
+The Reference Report includes the bibliographic citation, abstract, external IDs (PubMed, PubMed Central, DOI), and links to other FlyBase Report pages for any objects curated from the reference.
-The Reference Report includes the bibliographic citation, PubMed ID and abstract if available, and links to FlyBase report pages that contain data curated from the reference, where applicable.
+==Reference==
-Below is a field-by-field guide to the information provided within the Reference Report.
+This section provides the key bibliographic details about the reference.
-==Reference==
 {| class="wikitable" style="width: 100%;"
 |-
-|'''Citation'''	 || style="width: 80%;" | The bibliographic citation for the reference. The exact content of this field differs depending on publication type but, where applicable, the information is in the following order: authors (surname. initial), year, title, publication details (e.g. abbreviated journal name, volume and issue number), page range/article number/URL.
+| '''Header''' || style="width: 80%;" | Clicking on the 'Download as RIS’ icon at the end of the header line downloads a tagged text file of citation data that can be imported into any standard reference manager.
+|-
-For many journal articles, users can click on the hyperlinked section of the citation to be taken to the relevant webpage on the journal's server.
+|'''Citation'''	 || The exact content of this field differs by publication type but, where applicable, the information is in the following order: authors (surname. initials), year, title, journal abbreviation, volume, issue number, page range/article number/URL.
+Where available, the citation includes a hyperlink to the relevant webpage on the journal's website.
-The name of the parent publication (usually a journal or edited book) is presented in abbreviated form within the citation. The full name and some associated details are shown in the '''Parent Publication''' section of the Reference Report.
+|-
+|'''FlyBase ID'''	 || The unique FlyBase identifier for the reference (FBrf).
-Clicking on the 'Export to RIS’ link at the end of each citation downloads a tagged text file of citation data that can be imported into any standard reference manager.
 |-
-|'''FlyBase ID'''	 || The Primary FlyBase identifier number of the reference (FBrf), used to uniquely identify the reference in the database.
+|'''Publication Type'''	 || Term from the the [http://{{flybaseorg}}/cgi-bin/cvreport.pl?id=FBcv:0000189 publication class] section of the FlyBase Controlled Vocabulary.
-Any secondary FlyBase identifier numbers are listed in the '''Secondary IDs''' subsection of the '''Other Information''' section of the '''Reference Report'''.
 |-
-|'''Publication Type'''	 || The great majority of references within FlyBase are research papers from journals, but see the publication class section of the FlyBase controlled vocabulary for a full listing of publication types and their definitions.
+|'''Abstract'''	 || The abstract of the reference, usually obtained from PubMed.
 |-
-|'''ISBN'''	 || The 'International Standard Book Number' (ISBN) applies only to references of the publication type 'book'. It is a unique number which is widely used to catalogue and search for books. This subsection is only present if it has content.
+|'''PubMed ID'''	 || The PubMed identification (PMID) number for the reference, where available, hyperlinked to the relevant page at PubMed.
 |-
-|'''PubMed ID'''	 || The PubMed identification (PMID) number for the reference, where available. Clicking on the ID takes the user to the relevant page for the reference on the PubMed server.
+|'''PubMed Central ID'''	 || The PubMed Central identification (PMCID) number for the reference, where available.  Hyperlinks are provided both for NCBI PubMed Central and Europe PubMed Central.
 |-
-|'''PubMed Abstract'''	 || The abstract of the reference obtained from PubMed, where available.
+|'''DOI'''	 || The Digital Object Identifier for the reference, if available, hyperlinked to the relevant webpage on the journal's website.
 |-
-|'''Text of Personal Communication'''	 || The text of a 'personal communication to FlyBase' will appear here if available. If a digital copy of the communication is not available, the message 'Paper copy archived' will be shown and users can contact FlyBase for a copy. This subsection is only present if it has content. Any files that accompany the personal communication will be displayed in the '''Associated Files''' subsection of the '''Associated Information''' section.
+|'''ISBN'''	 || The 'International Standard Book Number' (ISBN) for references of the publication type 'book'. This field is only present if it has content.
 |-
-|'''DOI'''	 || The Digital Object Identifier for the reference, if available.
+|'''Text of Personal Communication'''	 || The text of a 'personal communication to FlyBase', if available. If unavailable, the message 'Paper copy archived' will be shown and users can contact FlyBase for a copy. This field is only present if it has content. Any files that accompany the personal communication will be displayed in the '''Associated Information''' section below.
 |}
-==Related Publications==
+==Related Publication(s)==
-This section lists any references in FlyBase that are directly linked to the subject of the Reference Report. Common examples of related publication types are:
+This section lists any references in FlyBase that are directly linked to the current Reference Report. Common examples of relationship types are:
-research paper and supplementary material
+* a research paper and an erratum
-research paper and erratum
+* a research paper and a commentary
-research paper and commentary
+* a research paper and a personal communication to FlyBase
-research paper and personal communication to FlyBase
+* a research paper and its supplementary material
+* distinct publications (e.g. a different languages and/or in a different journals) of the same paper in different formats (e.g. [http://{{flybaseorg}}/reports/FBrf0194405.html FBrf0194405])
-The publication type of the related reference is given in the left-hand column and the citation of the reference is provided in the right-hand column, along with its primary FlyBase identifier number. Clicking on this number will take users to the Reference Report of the related publication.
+Instances of the last example are displayed in a separate subsection titled 'Also Published As'.
+The publication type of the related reference is given in the left-hand column and the citation of that reference is provided in the right-hand column, with its FlyBase ID hyperlinked to the corresponding Reference Report.
 ==Recent Updates==
@@ Line 53: / Line 51: @@
 {| class="wikitable" style="width: 100%;"
 |-
-|'''Comments'''	 || style="width: 80%;" | A free text field used to provide comments that augment the basic citation details of a reference. This field is blank in most cases, but is often filled in for references of the type 'FlyBase analysis'.
+|'''Comments'''	 || style="width: 80%;" | Used by FlyBase curators to provide comments about the content of a reference. This field is blank in most cases, but is often filled in for references of the type 'FlyBase analysis'.
 |-
-|'''Associated Files'''	 || The names of, and links to, any files that accompany the subject of the Reference Report (usually a personal communication) but are not in text format and so cannot be displayed in situ. Entries are of the format "File date: xxx ; File size: xxx ; File format: (eg pdf) ; File name: (name)". Users can download the file by clicking on the hyperlinked name.
+|'''Associated Files'''	 || The names of, and links to, any files that accompany the given reference (usually a 'personal communication to FlyBase') but are not in text format and so cannot be displayed in situ (e.g. spreadsheets, images). Entries have the format "File date; File size; File format; File name".
 |}
@@ Line 62: / Line 60: @@
 {| class="wikitable" style="width: 100%;"
 |-
-|'''Secondary IDs'''	 || style="width: 80%;" | A list of secondary FlyBase identifier numbers of the reference. If a reference has a secondary identifier number, it generally indicates that at some point it has been merged with a duplicate entry in the database.
+|'''Secondary IDs'''	 || style="width: 80%;" | Any secondary FlyBase identifier (FBrf) number(s) used previously for the given reference. If present, this generally indicates that duplicate reference entries have been merged in the database.
-|-
-|'''Language of Publication'''	 || The language in which the main text (i.e. the non-abstract sections) of the publication is written. See the publication language section of the FlyBase controlled vocabulary for a full listing of publication languages used in FlyBase.
 |-
-|'''Additional Languages of Abstract'''	 || The abstract of a publication is sometimes provided in more than one language, even when the main text of the paper is in a single language. The additional language(s) of such abstracts are listed here.
+|'''Language of Publication'''	 || The [http://{{flybaseorg}}/cgi-bin/cvreport.pl?id=FBcv:0000234 language] in which the main text (i.e. the non-abstract sections) of the publication is written.
 |-
-|'''Also Published As''' || If the subject of the Reference Report also exists as a distinct publication in a different format (e.g. a different language) and/or in a different journal, then they will be listed here. The publication type and the citation of the other reference are shown, along with its primary FlyBase identifier number which is hyperlinked to its associated Reference Report.
+|'''Additional Languages of Abstract'''	 || Where the abstract of a publication is provided in more than one [http://{{flybaseorg}}/cgi-bin/cvreport.pl?id=FBcv:0000234 language] (even when the main text of the paper is in a single language), it is listed here.
 |}
 ==Parent Publication==
-Most references in FlyBase are not stand-alone publications, but are published within a 'parent publication' - usually a journal or an edited book. Details on the parent publication of the subject of the Reference Report are given in this section.
+Most references in FlyBase are not stand-alone publications, but are published within a 'parent publication' - usually a journal or sometimes an edited book. Details of the parent publication are given in this section.
 {| class="wikitable" style="width: 100%;"
 |-
-|'''Publication Type'''	 || style="width: 80%;" | The parent publication will be either 'journal', 'edited book', or the catch-all term 'compendium'. See the publication class section of the '''FlyBase controlled vocabulary''' for definitions.
+|'''Publication Type'''	 || style="width: 80%;" | Either 'journal', 'book', or the catch-all term 'compendium', taken from the [http://{{flybaseorg}}/cgi-bin/cvreport.pl?id=FBcv:0000189 publication class] section of the FlyBase Controlled Vocabulary.
 |-
-|'''Abbreviation'''	 || The abbreviation for the parent publication, used where the reference is cited in the '''Citation''' section of the '''Reference Report''' and in the '''References''' section of other Reports. Journal abbreviations usually mirror those used at PubMed.
+|'''Abbreviation'''	 || The FlyBase abbreviation for the parent publication. Journal abbreviations usually mirror those used at PubMed.
 |-
 |'''Title'''	 || The full title of the parent publication.
 |-
-|'''Editors'''	 || The editors where the parent publication is an edited book. Names are listed in the format "surname. initial". This subsection is only present if it has content.
+|'''Editors'''	 || The editor(s) where the parent publication is an edited book. Names are listed in the format "surname. initials". This field is only present if it has content.
 |-
-|'''Publication Year'''	 || The year in which an edited book was published, or the years of publication of a journal (only shown for older journals). This subsection is only present if it has content.
+|'''Publication Year'''	 || The year in which an edited book was published, or the years of publication of a journal (only shown for older journals). This field is only present if it has content.
 |-
-|'''ISBN/ISSN'''	 || The International Standard Book Number (ISBN) where the parent publication is an edited book, or the International Standard Serial Number (ISSN) where the parent publication is a journal. These are unique numbers that are widely used to catalogue and search for books and journals.
+|'''ISBN/ISSN'''	 || The International Standard Book Number (ISBN) where the parent publication is an edited book, or one or more International Standard Serial Numbers (ISSN) where the parent publication is a journal.
 |}
-==Data From Reference==
+==Data from Reference==
-This section provides a list of genetic objects (genes, alleles, aberrations, transgenic constructs etc.) that have been curated from the reference. Clicking on any of these takes the user directly to the respective report page. Genetic objects are listed as subsections according to type in alphabetical order. Subsections are only present where relevant data has been curated, meaning that this entire section will be blank for uncurated references, or will only have a 'Genes' subsection if they are the only type of object curated.
+This section provides a list of database objects (genes, alleles, aberrations, transgenic constructs etc.) that have been curated from the reference, each hyperlinked to their respective Report page. Objects are organized into subsections according to type and presented in alphabetical order. Subsections are only present where relevant data has been curated, meaning that this entire section will be blank for uncurated references, or will only have a 'Genes' subsection if that is the only object type curated.