Reference report help

Last Updated: 8 November 2006

The Reference Report includes the bibliographic citation, the National Library of Medicine's PubMed abstract if available, and links to FlyBase report pages that contain data curated from the reference, where applicable.

Below is a field-by-field guide to the information provided within the Reference Report.

The bibliographic citation for the reference. The exact format of this field differs depending on publication type, but where appropriate, the information is in the following order: authors (surname. initial), year, title, publication details (eg abbreviated journal name, volume and issue number), page numbers/URL.

For some journal articles, users can click on the hyperlinked section of the citation to be taken to the relevant webpage on the journal server, where they will be able to download the article. This will be similar to reaching such a page from other search engines and the ability of the user to download the article will depend on the terms and conditions of each particular journal server.

Book and journals names are presented in an abbreviated form within the citation. To see the full information for the book or journal, such as its full name and place of publication, see the PUBLISHED IN section of the Reference Report.

The Primary FlyBase identifier number of the reference, used to uniquely identify the reference in the database.

A reference may also have any number of Secondary FlyBase identifier numbers, which are listed in the Secondary IDs subsection of the OTHER REFERENCE INFORMATION section of the Reference Report.

The great majority of references within FlyBase are research papers and reviews from journals but there are an eclectic mix of references belonging to other publication types, e.g. letter, news article, poem.

For a full list of publication types, see the publication class section of the FlyBase controlled vocabulary.

The publication type 'letter' refers to scientific correspondence published within journals, not letters to FlyBase. Publications of the type 'personal communication to FlyBase' are correspondence sent to FlyBase either on paper or as an email message. The type 'news article' refers to articles appearing in commercial newspapers. The type 'review' covers any article or book chapter that reviews the literature and is more encompassing than the use of the term within many journals.

If this field is marked 'Yes', this means that an offprint of the reference is contained within the Drosophila Offprint Collection maintained by FlyBase (Cambridge), if 'No' then FlyBase does not hold a copy. Where users are unable to acquire a copy of a particular reference from a local library, laboratory, or inter-library loan, FlyBase will be happy to provide them with a copy of the reference. If the word 'Yes' is a hyperlink clicking it will take the user to a form that can be used to contact FlyBase and request a copy of that particular offprint. Otherwise offprints can be requested through the standard contact FlyBase form.

The PubMed (MEDLINE) accession number for the reference. Clicking on the ID takes the user to the relevant page for the reference on the PubMed server.

PubMed is a project developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It has been developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals at Web sites of participating publishers.

The abstract of the reference (obtained from PubMed), where available.

For references referring to the ADRC (Annual Drosophila Research Conference) or EDRC (European Drosophila Research Conference) the text of the abstract will be displayed in this field if available.

The Biosis identifier number for the reference, where available.

The Zoological record identifier number for the reference, where available.

A free text field used to provide comments that augment publication details. This field is blank for many reference reports but is often filled in for references that have been generated by FlyBase curators such as those of the type 'FlyBase analysis', 'personal communication to FlyBase' or 'computer file'.

When the Reference Report is of the type 'personal communication', the text of the personal communication may appear in full in this field. Personal communications that have been sent to FlyBase as e-mails will be shown in full, although e-mail adresses will be disguised and will be shown in the format name@XXXXXXXXXXXXX. Where text is not available, the message 'Paper copy archived' will be shown and users will be able to contact FlyBase for a full copy, using the offprint request system.

The names of, and links to, any files that accompany personal communications but are not in text format, and so cannot be displayed in the field above. 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.

A list of publications that are directly linked to the subject of the Reference Report. Common examples of related publications are:

• research paper and supplementary material
• research paper and erratum
• research paper and personal communication
• research paper and review
• Reviews are only linked to research papers in this way when the review is principally about 1 or 2 research papers in a 'News and Views' type format and does not simply indicate that the review cites the research paper.

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 the Primary FlyBase identifier number. Clicking on this number will take users to the Reference Report of the related publication.

Sometimes the same reference has been published more than once. A common reason for this is when references have been published in more than one language. In these cases, FlyBase assigns identifier numbers on a publication-by-publication basis rather than a reference-by-reference basis, so that each Reference Report contains only one citation and the citation for any other publications for each Reference Report are listed in this field. As with RELATED PUBLICATIONS, the reference type and full citation is listed and the Primary FlyBase identifier number is hyperlinked to take users straight to the Report corresponding to the other publication.

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 or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.

The language(s) in which the reference has been published.

In a number of publications, the abstracts for research papers are provided in more than one language, even when the main text of the paper is only in one language. The additional language(s) of such abstracts are listed here.

Applies only to references of the publication type 'book'. ISBN stands for International Standard Book Number, and is a unique number which is widely used to catalogue and search for books.

Applies only to references of the publication type 'book'. The place (usually city) of publication is listed.

This section applies to references that are not publications in their own right, but appear within other publications (referred to below as the parent publication). So, for all research papers, details on the journal or book in which the paper has been published are given here.

The FlyBase 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.

The abbreviations used are those of the World List of Scientific Periodicals Published in the Years 1900-1960 (4th edition, 1965) by P. Brown and G. B. Stratton (London, Butterworths Scientific Publications) for those published before 1960 and World List of Scientific Periodicals: New Periodical Titles 1960-1968 by K. J. Porter and C. J. Koster (London, 1970, Butterworths) for 1960 until 1968. We have tried to use the same conventions for the abbreviations of titles as followed in the World List for titles published after 1968, except that we have tried to be less imperialistic, and have made much use of the List of Serials Indexed for Online Users (National Library of Medicine, Washington 1992), the British-Union-Catalogue of Periodicals (London, 1955-1958) and its supplements, the Serial Publications in the British Museum (Natural History) Library (3rd ed. 1980), the Union List of Serials (3rd ed. 1965, H. W. Wilson, NY) and its successor the Library of Congress. New Serial Titles volumes (1950-) and Ulrich's International Periodical Directory 31st edition (1992-1993. R.R. Bowker, New Providence). We have used the Directory of Japanese Scientific Periodicals (National Diet Library, Tokyo, 1979) for the names of Japanese journals and Half a Century of Soviet Periodicals (R. Smits, Library of Congress, Washington 1968) for many of those of the Soviet Union (as was) (this publication includes US library holdings of these journals).

The full title of the parent publication.

The authors (or editors) of the parent publication. This field is most often filled in when a paper or review is published within a book. Names are listed in the format surname. initial.

Lists the volume number(s) of the parent publication, where applicable.

The year(s) in which the parent publication has been published.

The page range of the parent publication. Where the parent publication is a book the complete number of pages is listed here. Where books have a contents section numbered in Roman numerals, the number of pages in that section is also given. An example is ix + 409pp, where ix is the highest page number in the contents/introduction.

The name of the publisher is provided when the parent publication is not a journal.

The place (usually a city) where the parent publication has been published.

The language(s) in which the parent publication has been published.

The ISBN or ISSN of the parent publication. These are unique numbers given to publications and are widely used to by libraries and publishers to cite publications. ISBN stands for International Standard Book Number and applies only to books, while ISSN stands for International Standard Serial Number and applies to journals.

The CODEN identifier for the parent publication. A CODEN is a unique six letter code that is used to cite publications.

This section is only applicable to references that have been curated by FlyBase. It provides a list of genetic objects (aberrations, alleles, genes, transposons etc.) that have been curated from the reference. Clicking on any of these links the user directly to the report pages of these objects. Genetic objects are listed as subsections according to type in alphabetical order. The type of object is only listed where data has been curated so that this section will be blank for uncurated references or will only have the data type 'genes' where these are the only type of objects curated.