[oXygen-user] Reference managers for use with Oxygen?
Bernhard Kleine
bernhard.kleine at gmx.net
Tue Sep 4 06:34:24 CDT 2018
Am 03.09.2018 um 21:11 schrieb Da'ud Vyd:
> Did you use JebRef's Medline XML format for export?
Actually I developed my book in the docbook 5 format. The command line
'java -jar C:\Programme\JabRef4.2Test\JabRef-4.2Test.jar -o
cha04addBiB.xml,docbook -n true addkap04.bib'
converted the bib to docbook. The newer JabRef version 5 (in
development) does this by itself, but has only docbook 4.4 export.
Therefore, the file has to be edited:
1. id to xml:id
2. the xml:id is not allowed to contain "+", these had to be converted
to "."
3. between <author><firstname> and </surname></author> a tag personname
should be added
4. the ulink had to be changed
5. last not least I changed the xreflabel of every entry to "Loi et al.
(2001)" with two or three author to "Loi, Emmal und Park (2001)" for
the German edition. Most time consuming.
Most of these changes could be performed by a general search and
replace, only the fifth item had be done manually.
There is one caveat, not be left out. The bibtex (biblatex) format
depends heavily on braces. Scientic identifiers like Manduca sexta
(tobacco hawk moth) are enclosed in these braces. For unknown reason
such braced identifiers get lost, I have not tested this with the latest
version. The effect is that names are missing in titles.
The bibtex entry
> @Article{LEP+01,
> author = {Loi, P. K. and Emmal, S. A. and Park, Y. and
> Tublitz, N. J.},
> title = {Identification, sequence and expression of a
> crustacean cardioactive peptide (CCAP) gene in the moth Manduca sexta.},
> journaltitle = {J Exp Biol},
> date = {2001},
> volume = {204},
> number = {Pt 16},
> pages = {2803--16},
> eprint = {11683436},
> eprinttype = {pubmed},
> url = {http://jeb.biologists.org/content/204/16/2803.long},
> abstract = {The crustacean cardioactive peptide (CCAP) gene was
> isolated from the tobacco hawkmoth Manduca sexta. The gene has an open
> reading frame of 125 amino acid residues containing a single, complete
> copy of CCAP. Analysis of the gene structure revealed three introns
> interrupting the coding region. A comparison of the M. sexta CCAP gene
> with the Drosophila melanogaster genome database reveals significant
> similarities in sequence and gene structure. The spatial and temporal
> expression patterns of the CCAP gene in the M. sexta central nervous
> system were determined in all major post-embryonic stages using in
> situ hybridization techniques. The CCAP gene is expressed in a total
> of 116 neurons in the post-embryonic M. sexta central nervous system.
> Nine pairs of cells are observed in the brain, 4.5 pairs in the
> subesophageal ganglion, three pairs in each thoracic ganglion (T1-T3),
> three pairs in the first abdominal ganglion (A1), five pairs each in
> the second to sixth abdominal ganglia (A2-A6) and 7.5 pairs in the
> terminal ganglion. The CCAP gene is expressed in every ganglion in
> each post-embryonic stage, except in the thoracic ganglia of first-
> and second-instar larvae. The number of cells expressing the CCAP gene
> varies during post-embryonic life, starting at 52 cells in the first
> instar and reaching a maximum of 116 shortly after pupation. One set
> of thoracic neurons expressing CCAP mRNA shows unusual variability in
> expression levels immediately prior to larval ecdysis. Using
> previously published CCAP immunocytochemical data, it was determined
> that 91 of 95 CCAP-immunopositive neurons in the M. sexta central
> nervous system also express the M. sexta CCAP gene, indicating that
> there is likely to be only a single CCAP gene in M. sexta.},
> language = {eng},
> authoraddress = {Institute of Neuroscience, University of Oregon,
> Eugene 97403, USA. tublitz at uoneuro.uoregon.edu},
> file =
> {JExpBiol_204_2803_loi.pdf:1_comp_endo/Invertebrata_Neuropeptides_selected/CCAP/JExpBiol_204_2803_loi.pdf:PDF},
> groups = {Kap05},
> keywords = {Amino Acid Sequence ; Animals ; Base Sequence ;
> Drosophila melanogaster/genetics ; Ganglia, Invertebrate/chemistry ;
> *Gene Expression ; Manduca/*genetics/growth \& development/metabolism
> ; Molecular Sequence Data ; Nervous System/embryology/growth \&
> development/metabolism ; Neuropeptides/*analysis/chemistry/*genetics ;
> Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment},
> medline-da = {20011030},
> medline-dcom = {20020124},
> medline-edat = {2001/10/31 10:00},
> medline-fau = {Loi, P K ; Emmal, S A ; Park, Y ; Tublitz, N J},
> medline-is = {0022-0949 (Print)},
> medline-jid = {0243705},
> medline-jt = {The Journal of experimental biology},
> medline-lr = {20061115},
> medline-mhda = {2002/01/25 10:01},
> medline-own = {NLM},
> medline-pl = {England},
> medline-pst = {ppublish},
> medline-pt = {Comparative Study ; Journal Article ; Research
> Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ;
> Research Support, U.S. Gov't, P.H.S.},
> medline-pubm = {Print},
> medline-rn = {0 (Neuropeptides) ; 0 (crustacean cardioactive
> peptide)},
> medline-sb = {IM},
> medline-so = {J Exp Biol. 2001 Aug;204(Pt 16):2803-16.},
> medline-stat = {MEDLINE},
> owner = {bk},
> timestamp = {1900.01.01},
> }
The converted xml entry
**
> <?xml version='1.0' encoding='UTF-8'?>
> <!DOCTYPE bibliography PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
> "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd">
> <!-- This file was exported from JabRef -->
> <bibliography>
> <biblioentry xreflabel="LEP+01" id="LEP+01">
> <authorgroup>
> <author><firstname>P. K.</firstname><surname>Loi</surname></author>
> <author><firstname>S.
> A.</firstname><surname>Emmal</surname></author>
> <author><firstname>Y.</firstname><surname>Park</surname></author>
> <author><firstname>N.
> J.</firstname><surname>Tublitz</surname></author>
>
> </authorgroup>
> <citetitle pubwork="article">Identification, sequence and
> expression of a crustacean cardioactive peptide (CCAP) gene in the
> moth Manduca sexta.</citetitle>
> <citetitle pubwork="journal">J Exp Biol</citetitle>
>
> <volumenum>204</volumenum>
>
> <artpagenums>2803–16</artpagenums>
> <pubdate>2001</pubdate>
> <bibliomisc><ulink
> url="http://jeb.biologists.org/content/204/16/2803.long">http://jeb.biologists.org/content/204/16/2803.long</ulink></bibliomisc>
> <abstract>
> <para>The crustacean cardioactive peptide (CCAP) gene was
> isolated from the tobacco hawkmoth Manduca sexta. The gene has an open
> reading frame of 125 amino acid residues containing a single,
> complete copy of CCAP. Analysis of the gene structure revealed three
> introns interrupting the coding region. A comparison of the M. sexta
> CCAP gene with the Drosophila melanogaster genome database reveals
> significant similarities in sequence and gene structure. The spatial
> and temporal expression patterns of the CCAP gene in the M. sexta
> central nervous system were determined in all major post-embryonic
> stages using in situ hybridization techniques. The CCAP gene is
> expressed in a total of 116 neurons in the post-embryonic M. sexta
> central nervous system. Nine pairs of cells are observed in the
> brain, 4.5 pairs in the subesophageal ganglion, three pairs in
> each thoracic ganglion (T1-T3), three pairs in the first
> abdominal ganglion (A1), five pairs each in the second to sixth
> abdominal ganglia (A2-A6) and 7.5 pairs in the terminal ganglion.
> The CCAP gene is expressed in every ganglion in each
> post-embryonic stage, except in the thoracic ganglia of
> first- and second-instar larvae. The number of cells
> expressing the CCAP gene varies during post-embryonic life,
> starting at 52 cells in the first instar and reaching a maximum of 116
> shortly after pupation. One set of thoracic neurons expressing CCAP
> mRNA shows unusual variability in expression levels immediately prior
> to larval ecdysis. Using previously published CCAP immunocytochemical
> data, it was determined that 91 of 95 CCAP-immunopositive
> neurons in the M. sexta central nervous system also express the M.
> sexta CCAP gene, indicating that there is likely to be only a
> single CCAP gene in M. sexta.
> </para>
> </abstract>
> </biblioentry>
> </bibliography>
--
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www.b-kleine.com, www.urseetal.net
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