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Welcome. Monday, 21-Jan-19 21:41
 
The JESS literature reference (JLR) sub-system is employed to store
and manipulate bibliographic data. It is used in particular by us
to deal with literature references for the JESS Parent Database
(JPD) which holds the current version of all the thermodynamic data
we have compiled from the literature. It can also be used by you to
develop one or more databases with literature references of
personal interest to you.
 
 

The main features of our literature reference system are as follows. * Literature references generally comprise the bibliographic specification (e.g. journal, year, volume, first-page), the names of the authors, the title (or heading) of the paper, the last page and a selected set of keywords. * A summary of the paper, or other textual information, can be associated with each reference * Conventions exist for dealing with monographs, reports etc. and with chapters in edited books.
The following is a very brief description of what the more important JLR programs do. Consult the index for more detail about specific programs. The most frequently used programs VEWJLR - Permits viewing of the database. The program accesses the database as "read only" so the database cannot be corrupted by incorrect usage, power failures, etc. UPDJLR - Permits updating of the database. DMTJLR - Dismounts a database producing a set of sequential files containing all the information in the database. The database can be reconstructed from these files using program MNTJLR. MNTJLR - Mounts a database from the *.ARC files produced by program DMTJLR. Consult the index searching for the term "mount" to obtain more details about the mount/demount procedure and the need for it. Less frequently used programs BLDJLR - Builds a new database from the *.ARC files produced by program DMTJLR. Reconstructs all internal links of the database (cf MNTJLR which does not and thus executes significantly faster). FMTJLR - Produces a file of output for printing with all the literature references formatted according to instructions which are usually invoked from a standard set of files but may also be specifically prepared by you. GBLJLR - Permits certain modifications to be made to the database which are of a "global" nature (i.e. affect more than just one reference). VFYJLR - Permits special checking operations, concerned with the integrity of the database and of the correct format for the names of scientific journals. PUTJLR - Produces a JLR "transfer file" - the *.WRK file used to move literature reference data to another computer. GETJLR - Inserts data from a JLR "transfer file" into an existing JLR database.
Special conventions are employed by the JLR sub-system in the abbreviation of data items. These allow you to specify things which already exist in the database with a relatively few key strokes. You need to be familiar with the rules governing such abbreviations before you use any JLR program. Once you have learned these rules you will find that they provide a powerful interface for interogating the database. On the other hand, you are likely to find yourself frustrated if you attempt to employ the JLR programs before familiarizing yourself with the abbreviation conventions. Abbreviations for References Reference identifiers can be abbreviated simply by leaving off a trailing part of the identifier. In the limit, only the publication name and the year of publication have to be entered. If you enter an abbreviation that matches more than one reference, a menu will be displayed and you will be asked to select the particular reference you require. Examples can be found in the JESS Primer. Other JLR Abbreviations Other JLR data items (namely author names, publications and keywords) can also be abbreviated. In these cases, the rules are: (i) that any trailing part of the name may be omitted; (ii) only those names that match the pattern of uppercase letters supplied will be considered - lowercase letters and punctuation symbols can thus be omitted from the given abbreviation. Further examples can be found in the JESS Primer.
The JLR sub-system supports the association of certain words and phrases with sets of literature references. These are called keywords. At present the keywords which have been introduced into the literature reference part of the JESS thermodynamic database (JPD) are in a rather unsatisfactory state. Search the index for "deficiency" (without quotes) for more details. The keywords which have been included so far are based on the JESS chemistry thesaurus. This specifies the keywords which have been selected in preference to others that are similar and may be thought of instead by you. The thesaurus also gives some terms that are conceptually closely related and it defines an hierachical structure of keywords, giving broader or narrower terms where appropriate. We hope this approach will ultimately help to bridge the gap between the philosophy of those choosing the keyords (the "keyworder") and those wishing to retrieve literature references from the literature database by keyword (the "keywordee" - or should that be the "searcher"?!)
Program FMTJLR is used by you to produce printable output of literature references with almost any format you require. Program FMTJLR takes instructions about the format to use from a sequential file named by you. Many such files have been pre-prepared so that you can probably achieve the result you want with ease. The following files of formating instructions are available so far. (Please let us know if you think they can be improved in any way.) File name Journal for which format applies V/ACA Anal. Chim. Acta V/AEMICR Appl. Exp. Microbiol. V/GCA Geochim. Cosmochim. Acta V/GRANTI (General format with headings & JLR sequence number, indented) V/GRANTN (General format with headings & JLR sequence number, not indented) V/GRANTX (General format with headings & JLR UIDs) V/GRANTY (General format with headings & JLR UIDs & JLR reference numbers) V/ICA Inorg. Chim. Acta V/JACS J. Am. Chem. Soc. V/JBC J. Biol. Chem. V/JCSD J. Chem. Soc. Dalton Trans. V/LANCET Lancet V/NATURE Nature V/PHRMRV Pharmacol. Rev. V/POLYH Polyhedron V/TALANT Talanta Producing a file with formatting instructions If none of the above files suits your purpose you can produce a file for yourself with the necessary formatting instructions for program FMTJLR. This files is always comprised of four sections, each of which is headed by a line specifying what follows. The first section concerns the style and layout of the author names (applicable to all the literature references that are processed); it is somewhat different from the remaining sections, which are essentially similar and concern the way that the three types of JLR reference are formatted. The layout of the file is accordingly as follows. Author format ----- ----- ----- Reference format ----- ----- ----- Chapter format ----- ----- ----- Book format ----- ----- ----- The actual formatting instructions, indicated above by the dashes, depend on certain significant concepts which you must understand thoroughly before preceding. Most important of these is the notion that each record (or line) in the section is treated as a "field", which generally (but not always) is associated with some item of data from the reference. The number of these fields is up to you and is entirely variable. The format you require determines their content and their order: program FMTJLR works systematically through the given fields in turn, finding the associated data and writing it to the output file when its field is processed. By convention, the data items associated with each field are indicated by a two-character code. The first character of this code is always an ampersand character, &. The second is an UPPERCASE letter that identifies the type of data. Thus, for example, the year in which the reference was published is indicated by the code "&Y". This code may be placed anywhere in its own field (i.e on its own line) and surrounded by appropriate spacing and punctuation. The program simply substitutes the four digits (comprising the year of the reference) in place of the "&Y". The following two-character codes are recognized. &A author(s) &C company (i.e. publisher of book and location) &E editor(s) &F first page number of article &H heading of article &I indented sequence number (i.e. position of reference in output list, right justified over 4 columns) &K the JLR filing code or data number &L last page number of article &N number of reference (in the database) &P publication (journal or book name) &S subtitle of book &T text of reference summary &U unindented sequence number (i.e. position of reference in output list, inserted without justification) &V volume of journal &Y year of publication Note that if the kind of data specified by the two-character code is not available for that reference, the whole field (i.e. including any punctuation) is omitted from the output. On the other hand, if a field is not associated with any particular kind of data (i.e. it does not contain a two-character code) then the punctuation (and any other characters) contained in the field are always included in the output. To illustrate how things work in a very simple situation, consider the following part of a file of formatting instructions. ----- Reference format &P (&Y) &V, &F -&L . Chapter format ----- This produces references that would appear as follows. Geochim. Cosmochim. Acta (1987) 51, 597-605. Anal. Chim. Acta (1978) 101, 339. Chemsa (1978) 170-172. Observe that in the second case there is no last page and, in the third case, there is no volume number. Note also that the blank space before the year, volume and first-page fields is important.