############################################################
# CB2BIB/EDITOR BOOKMARKS AND NETWORK QUERY INFORMATION FILE
############################################################

###########
# BOOKMARKS
###########
# Syntax:
# bookmark=Description|Target URL
# Notes:
# - cb2Bib tags, e. g. BibTeX fields enclosed as <<...>>, can be included in the URL. These tags will be
#   substituted by the current values.
# - The non BibTeX tag <<selection>> is the placeholder for the current text selection.
# - Some special characters, such as |, might need percent encoding to properly work.
# Bookmark Examples:
bookmark=PubMed Citation Finder|https://pubmed.ncbi.nlm.nih.gov/citmatch/
bookmark=DBLP Bibliography|https://dblp.org/search/
bookmark=arXiv.org e-Print archive|https://arxiv.org/
bookmark=CiteSeerX|https://citeseerx.ist.psu.edu/
bookmark=Directory of Open Access Journals|https://doaj.org/search
bookmark=PLoS - The Public Library of Science|https://www.plos.org/
bookmark=OAIster|https://www.oclc.org/en/oaister.html
bookmark=Search ACS Publications|https://pubs.acs.org/search/advanced
bookmark=Google Scholar|https://scholar.google.com/
bookmark= |
bookmark=Search arXiv for selected text|https://search.arxiv.org:8081/?query=<<selection>>
bookmark=Search CiteSeerX for Title|https://citeseerx.ist.psu.edu/search?q=title%3A<<title>>&sort=cite
bookmark=Search PubMed for Title|https://www.ncbi.nlm.nih.gov/pubmed?term=<<title>>
bookmark=Search PubMed for DOI|https://www.ncbi.nlm.nih.gov/pubmed?term=<<doi>>
bookmark=Search Google for literal Title|https://www.google.com/search?ie=UTF-8&q=%22<<title>>%22
bookmark=Search Scholar for literal Title|https://scholar.google.com/scholar?ie=UTF-8&q=%22<<title>>%22
bookmark=Search Crossref for Journal + Volume + Page|https://www.crossref.org/guestquery/?search_type=journal&auth=&issn=&title=<<journal>>&art_title=&volume=<<volume>>&page=<<pages>>&isbn=&comp_num=&series_title=&multi_hit=on&view_records=Search
bookmark=Search ISBN Database|https://isbndb.com/search-all.html?kw=<<isbn>>
bookmark=Open DOI Document|https://doi.org/<<doi>>

##################
# EDITOR BOOKMARKS
##################
# Syntax:
# editorbookmark=Description|Target file name|Shortcut|Icon file name
# Bookmark Example:
editorbookmark=Bookmarks Description|https://www.molspaces.com/cb2bib/doc/bibeditor/#bookmarks||

###########################
# NETWORK QUERY INFORMATION
###########################
# Description:
# The cb2Bib tags
#            <<journal>>,
#            <<volume>>,
#            <<pages>>,
#            <<eprint>>,
#            <<doi>>,
# and/or
#            <<excerpt>>
# are substituted in the Submission Form (see below) by the actual values of the
# reference.
# 1) In a first step, the 'query' URL containing above substituted tags is sent to the
# database server or publisher's website.
# 2) Once the URL is retrieved, in a second step, cb2Bib captures a database identifier
# for the desired reference. This step is a regular expression caption.
#
# Steps 1) and 2) are therefore a mapping from the given reference fields to the server
# database identifier.
#
# 3) In the next step the server identifier is used to retrieve the complete
# bibliographic reference,
# 4) and possibly the link or URL for the target document, usually a PDF file.
#
#
# In summary, queries are performed in these 4 steps:
# 1)  Post Query( journal-fullname, volume, first page; or doi; or excerpt ) (HTML post +
#     cb2Bib tags)
# 2)  Capture referenceurl and pdfurl from query (RegExp)
# 3)  Retrieve referenceurl = referenceurl_prefix + capture_from_query + referenceurl_sufix
# 4)  Schedule for retrieving pdfurl = pdfurl_prefix + capture_from_query + pdfurl_sufix
#
# NOTE: If pdfurl_prefix contains a cb2Bib tag, for example
#       pdfurl_prefix=http://example.com/<<doi>>
#       then pdfurl will be formed by substituting <<doi>> instead of capture_from_query
#
# NOTE: For the single query cases with no htm2txt_query and referenceurl_prefix
#       capture_from_query can be used for checking the suitability of the query
#       result
#
#--------------------------------------------------------------------------------------------
# Submission Form
# All field/lines required, ordered as here, no comment or blank lines in between
#--------------------------------------------------------------------------------------------
# QUERY INFO FOR
#journal=cb2Bib Long Journal Name|journal code (or left blank if none needed, see ACS example)
#query=  (use '<<post>>http://www...' for http post method, instead of get method)
#capture_from_query=
#referenceurl_prefix=
#referenceurl_sufix=
#pdfurl_prefix=
#pdfurl_sufix=
#action=
#
#--------------------------------------------------------------------------------------------
# ACTION Description:
#--------------------------------------------------------------------------------------------
#
#  blank = cb2Bib imports query output to clipboard panel and deletes previous panel contents
#  merge_all_metadata = cb2Bib appends query and referenceurl output to clipboard panel
#  merge_referenceurl_metadata = cb2Bib appends referenceurl output to clipboard panel
#  browse_query = cb2Bib opens the url in query
#  browse_referenceurl = cb2Bib opens referenceurl_prefix + capture_from_query + referenceurl_sufix
#
#  Perform HTML to text conversion before importing to clipboard panel:
#  htm2txt_query = cb2Bib imports the url in query
#  htm2txt_referenceurl = cb2Bib imports referenceurl_prefix + capture_from_query + referenceurl_sufix
#
#--------------------------------------------------------------------------------------------
# Examples below explain and clarify the query syntax
#--------------------------------------------------------------------------------------------

# Check arXiv for <<eprint>>, if DOI is returned check CR, merge_all_metadata for a complete
# bibliographic record, and schedule PDF download
journal=
query=https://export.arxiv.org/api/query?id_list=<<eprint>>
capture_from_query=>(10\.\d[^<]+)<
referenceurl_prefix=https://api.crossref.org/works/
referenceurl_sufix=
pdfurl_prefix=https://arxiv.org/pdf/<<eprint>>
pdfurl_sufix=
action=merge_all_metadata

# Check arXiv for <<eprint>>, use capture_from_query to ensure received data is correct,
# schedule PDF download
journal=
query=https://export.arxiv.org/api/query?id_list=<<eprint>>
capture_from_query=arxiv\.org/abs/(<<eprint>>)
referenceurl_prefix=
referenceurl_sufix=
pdfurl_prefix=https://arxiv.org/pdf/<<eprint>>
pdfurl_sufix=
action=merge_all_metadata

# Check PubMed for <<doi>> and schedule PDF download if available
journal=
query=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=<<doi>>&field=doi&retmode=xml
capture_from_query=<Id>(\d+)</Id>
referenceurl_prefix=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&report=xml&format=text&id=
referenceurl_sufix=
pdfurl_prefix=https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=

# Check CR for <<doi>>, use merge_all_metadata to keep clipboard contents for a manual
# extraction of the abstract
journal=
query=https://api.crossref.org/works/<<doi>>
capture_from_query=("status":.*"ok")
referenceurl_prefix=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=merge_all_metadata

# Check PubMed for <<journal>>|<<volume>>|<<pages>>, use journal to set specific codes for
# specific journals
journal=Proteins: Structure, Function, and Bioinformatics|Proteins
journal=Proteins: Structure, Function, and Genetics|Proteins
query=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=<<journal>>||<<volume>>|<<pages>>||c2bquery|
capture_from_query=c2bquery\|(\d+)\b
referenceurl_prefix=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&report=xml&format=text&id=
referenceurl_sufix=
pdfurl_prefix=https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=

# Check PubMed for <<journal>>|<<volume>>|<<pages>> for any journal
journal=
query=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi?db=pubmed&retmode=xml&bdata=<<journal>>||<<volume>>|<<pages>>||c2bquery|
capture_from_query=c2bquery\|(\d+)\b
referenceurl_prefix=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&report=xml&format=text&id=
referenceurl_sufix=
pdfurl_prefix=https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=

# Check CR for <<journal>>|<<volume>>|<<pages>> 
journal=
query=https://www.crossref.org/guestquery?search_type=journal&auth=&issn=&title=<<journal>>&art_title=&volume=<<volume>>&issue=&page=<<pages>>%20&year=&isbn=&comp_num=&series_title=&multi_hit=on&view_records=Search&queryType=bibsearch
capture_from_query=>\s*http://dx\.doi\.org/(.+)
referenceurl_prefix=https://api.crossref.org/works/
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=merge_referenceurl_metadata

# At this point all previous searches had been unsuccessful, then use the clipboard contents
# summary, <<excerpt>> tag, for browsing a generic internet search
journal=
query=https://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<excerpt>>&btnG=Search
capture_from_query=
referenceurl_prefix=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_query

%c2b_stop_parsing

#--------------------------------------------------------------------------------------------
# Examples below are deprecated, they are kept here to further clarify the query syntax
#--------------------------------------------------------------------------------------------

# QUERY INFO FOR IJQC
# No BibTeX reference available. Instead, set 'action=browse_referenceurl'.
# Reference and PDF file can later be extracted from browser, by selecting it.
journal=International Journal of Quantum Chemistry|
query=http://www3.interscience.wiley.com/search/allsearch?mode=citation&contextLink=%3Ca+href%3D%22%2Findex.html%22+target%3D%22_top%22%3EHome%3C%2Fa%3E+%2F+%3Ca+href%3D%22%2Fcgi-bin%2Fbrowsebysubject%3Fcode%3DCHEM%22+target%3D%22_top%22%3EChemistry%3C%2Fa%3E+%2F+%3Ca+href%3D%22%2Fcgi-bin%2Fbrowsebycategory%3Fcode%3DCH65%22+target%3D%22_top%22%3EComputational+Chemistry+and+Molecular+Modeling%3C%2Fa%3E&issn=1097-461X&volume=<<volume>>&issue=&pages=<<pages>>
capture_from_query=/journal/(\d+)/abstract
referenceurl_prefix=http://www3.interscience.wiley.com/journal/
referenceurl_sufix=/abstract
pdfurl_prefix=
pdfurl_sufix=
action=browse_referenceurl

# QUERY INFO FOR PNAS (Volume and Page)
# Extracts BibTeX reference and article PDF file
journal=Proceedings of the National Academy of Sciences of the United States of America|
query=http://www.pnas.org/search?submit=yes&submit=Submit&pubdate_year=&volume=<<volume>>&firstpage=<<pages>>&doi=&author1=&author2=&title=&andorexacttitle=and&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=Jan&fyear=1915&tmonth=Jul&tyear=2024&tocsectionid=all&format=standard&hits=10&sortspec=relevance&submit=yes
capture_from_query=/content/(.+)\.(extract|abstract|full)
referenceurl_prefix=http://www.pnas.org/citmgr?type=bibtex&gca=pnas;
referenceurl_sufix=
pdfurl_prefix=http://www.pnas.org/content/
pdfurl_sufix=.full.pdf
action=

# QUERY INFO FOR PNAS (DOI)
# Extracts BibTeX reference and article PDF file
journal=Proceedings of the National Academy of Sciences of the United States of America|
query=http://www.pnas.org/search?submit=yes&submit=Submit&doi=<<doi>>
capture_from_query=/content/(.+)\.(extract|abstract|full)
referenceurl_prefix=http://www.pnas.org/citmgr?type=bibtex&gca=pnas;
referenceurl_sufix=
pdfurl_prefix=http://www.pnas.org/content/
pdfurl_sufix=.full.pdf
action=

# QUERY INFO FOR BIOMETRIKA
# Extracts BibTeX reference
journal=Biometrika|
query=http://biomet.oxfordjournals.org/cgi/search?sendit=Search&pubdate_year=&volume=<<volume>>&firstpage=<<pages>>&DOI=&author1=&author2=&title=&andorexacttitle=and&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=Jan&fyear=&tocsectionid=all&RESULTFORMAT=1&hits=10&hitsbrief=25&sortspec=relevance&sortspecbrief=relevance
capture_from_query=http://biomet\.oxfordjournals\.org/cgi/content/abstract/([/\d\w]+)\?
referenceurl_prefix=http://biomet.oxfordjournals.org/cgi/citmgr?type=bibtex&gca=biomet;
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=

# QUERY INFO FOR NAR
# Extracts BibTeX reference and article PDF file
journal=Nucleic Acids Research|
query=http://nar.oxfordjournals.org/cgi/search?sendit=Search&pubdate_year=&volume=<<volume>>&firstpage=<<pages>>&DOI=&author1=&author2=&title=&andorexacttitle=and&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=Jan&fyear=1990&tocsectionid=all&RESULTFORMAT=1&hits=10&hitsbrief=25&sortspec=relevance&sortspecbrief=relevance
capture_from_query=http://nar\.oxfordjournals\.org/cgi/content/abstract/([/\d\w]+)\?
referenceurl_prefix=http://nar.oxfordjournals.org/cgi/citmgr?type=bibtex&gca=nar;
referenceurl_sufix=
pdfurl_prefix=http://nar.oxfordjournals.org/cgi/reprint/
pdfurl_sufix=.pdf
action=

# QUERY INFO FOR B
# Extracts BibTeX reference and article PDF file
journal=Bioinformatics|
query=http://bioinformatics.oxfordjournals.org/cgi/search?sendit=Search&pubdate_year=&volume=<<volume>>&firstpage=<<pages>>&DOI=&author1=&author2=&title=&andorexacttitle=and&titleabstract=&andorexacttitleabs=and&fulltext=&andorexactfulltext=and&fmonth=Jan&fyear=1990&tocsectionid=all&RESULTFORMAT=1&hits=10&hitsbrief=25&sortspec=relevance&sortspecbrief=relevance
capture_from_query=http://bioinformatics\.oxfordjournals\.org/cgi/reprint/([/\d\w]+)\?
referenceurl_prefix=http://bioinformatics.oxfordjournals.org/cgi/citmgr?type=bibtex&gca=bioinfo;
referenceurl_sufix=
pdfurl_prefix=http://bioinformatics.oxfordjournals.org/cgi/reprint/
pdfurl_sufix=.pdf
action=

# QUERY INFO FOR PubMed
# Extracts Medline reference
# Blank journal meaning 'any journal name'
journal=
query=http://www.ncbi.nlm.nih.gov/pubmed?term=<<doi>>
capture_from_query=\bPMID:\D{1,10}(\d+)\D
referenceurl_prefix=http://www.ncbi.nlm.nih.gov/pubmed/
referenceurl_sufix=?report=xml&format=text
pdfurl_prefix=http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=htm2txt_referenceurl

# QUERY INFO FOR PubMed, SPECIAL CASES (PubMed doesn't know full journal name)
# Extracts Medline reference
journal=Proteins: Structure, Function, and Bioinformatics|Proteins
journal=Proteins: Structure, Function, and Genetics|Proteins
query=http://www.ncbi.nlm.nih.gov/pubmed?term=<<journal>>[Jour]+AND+<<volume>>[volume]+AND+<<pages>>[page]
capture_from_query=\bPMID:\D{1,10}(\d+)\D
referenceurl_prefix=http://www.ncbi.nlm.nih.gov/pubmed/
referenceurl_sufix=?report=xml&format=text
pdfurl_prefix=http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=htm2txt_referenceurl

# QUERY INFO FOR PubMed
# Extracts Medline reference
# Blank journal meaning 'any journal name'
journal=
query=http://www.ncbi.nlm.nih.gov/pubmed?term=<<journal>>[Jour]+AND+<<volume>>[volume]+AND+<<pages>>[page]
capture_from_query=\bPMID:\D{1,10}(\d+)\D
referenceurl_prefix=http://www.ncbi.nlm.nih.gov/pubmed/
referenceurl_sufix=?report=xml&format=text
pdfurl_prefix=http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=htm2txt_referenceurl

# QUERY INFO FOR ACS
# Point to the abstract page.
journal=Accounts of Chemical Research|achre4
journal=ACS Applied Materials and Interfaces|aamick
journal=Analytical Chemistry|ancham
journal=Analytical Chemistry A-Pages|anchama
journal=Biochemistry|bichaw
journal=Bioconjugate Chemistry|bcches
journal=Biomacromolecules|bomaf6
journal=Biotechnology Progress|bipret
journal=Chemical Research in Toxicology|crtoec
journal=Chemical Reviews|chreay
journal=Chemistry of Materials|cmatex
journal=Crystal Growth and Design|cgdefu
journal=Energy and Fuels|enfuem
journal=Environmental Science and Technology A-Pages|esthaga
journal=Environmental Science and Technology|esthag
journal=Industrial and Engineering Chemistry|iechad
journal=Industrial and Engineering Chemistry Research Fundamentals|iecfa7
journal=Industrial and Engineering Chemistry Research|iecred
journal=Inorganic Chemistry|inocaj
journal=Journal of Agricultural and Food Chemistry|jafcau
journal=Journal of Chemical and Engineering Data|jceaax
journal=Journal of Chemical Information and Computer Sciences|jcisd8
journal=Journal of Chemical Information and Modeling|jcisd8
journal=Journal of Chemical Theory and Computation|jctcce
journal=Journal of Combinatorial Chemistry|jcchff
journal=Journal of Medicinal Chemistry|jmcmar
journal=Journal of Natural Products|jnprdf
journal=Journal of Organic Chemistry|joceah
journal=The Journal of Physical Chemistry A|jpcafh
journal=The Journal of Physical Chemistry B|jpcbfk
journal=The Journal of Physical Chemistry C|jpccfk
journal=Journal of Physical Chemistry|jpchax
journal=Journal of Proteome Research|jprobs
journal=Journal of the American Chemical Society|jacsat
journal=Langmuir|langd5
journal=Macromolecules|mamobx
journal=Molecular Pharmaceutics|mpohbp
journal=Nano Letters|nalefd
journal=Organic Letters|orlef7
journal=Organic Process Research and Development|oprdfk
journal=Organometallics|orgnd7
query=http://pubs.acs.org/action/quickLink?quickLinkJournal=<<journal>>&quickLinkVolume=<<volume>>&quickLinkPage=<<pages>>&cookieSet=1
capture_from_query=
referenceurl_prefix=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_query

# QUERY INFO FOR JCP, JAP and JMP
# Extracts BibTeX reference
journal=The Journal of Chemical Physics|JCP
journal=Journal of Chemical Physics|JCP
journal=Journal of Applied Physics|JAP
journal=Journal of Mathematical Physics|JMP
query=http://link.aip.org/link/?<<journal>>/<<volume>>/<<pages>>
capture_from_query=filetype=pdf&id=([\w\d]+)&
referenceurl_prefix=http://scitation.aip.org/getabs/servlet/GetCitation?fn=view_bibtex2&source=scitation&PrefType=ARTICLE&PrefAction=Add+Selected&SelectCheck=
referenceurl_sufix=&downloadcitation=+Go+
pdfurl_prefix=http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=
pdfurl_sufix=&idtype=cvips
action=

# QUERY INFO FOR DOI
# If DOI is known, and so far the reference is not found, at least browse reference
journal=
query=http://dx.doi.org/<<doi>>
capture_from_query=
referenceurl_prefix=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_query

# QUERY INFO FOR CR
journal=
query=http://www.crossref.org/guestquery?search_type=journal&auth=&issn=&title=<<journal>>&art_title=&volume=<<volume>>&issue=&page=<<pages>>%20&year=&isbn=&comp_num=&series_title=&multi_hit=on&view_records=Search&queryType=bibsearch
capture_from_query=>\s*http://dx\.doi\.org/(.+)
referenceurl_prefix=http://dx.doi.org/
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_referenceurl

# QUERY INFO FOR PubMed
# Extracts Medline reference
# Uses <<title>> tag
journal=
query=http://www.ncbi.nlm.nih.gov/pubmed?term=<<title>>
capture_from_query=\bPMID:\D{1,10}(\d+)\D
referenceurl_prefix=http://www.ncbi.nlm.nih.gov/pubmed/
referenceurl_sufix=?report=xml&format=text
pdfurl_prefix=http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/
pdfurl_sufix=/pdf/
action=htm2txt_referenceurl

# QUERY INFO FOR Google Scholar
journal=
query=https://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<doi>>&btnG=Search
capture_from_query=info:(\w+):scholar
referenceurl_prefix=https://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=

# QUERY INFO FOR Google Scholar
# Uses <<excerpt>> tag
journal=
query=https://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<excerpt>>&btnG=Search
capture_from_query=info:(\w+):scholar
referenceurl_prefix=https://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=
