When creating HighWire (arthw.dtd) SGML, when using the element
inter-refthere are a variety of currently supported codes that can be used in
locator-typeattribute to identify links to external databases. These are:
gen-- NCBI's nucleotide database
genpept-- NCBI's protein database
pirdb-- Protein Information Resource
mmdb-- NCBI's structure database (Molecular Modeling DataBase)
omim-- NCBI's Online Mendelian Inheritance in Man
ec-- Enzyme Collection
sprot-- SwissProt (ExPASy Molecular Biology Server)
pdb-- Protein Data Bank (formerly Brookhaven Data Bank)
ncbigeo-- NCBI's GEO (Gene Expression Omnibus) database
inter-refelement would be as follows:
<inter-ref locator="A23187" locator-type="gen">A23187</inter-ref>
If the files cannot be tagged using
inter-ref to identify database links, the HighWire parsing system (HPS) will make an attempt to resolve links to NCBI's nucleotide links on its own. It creates the links only if a certain pattern in the sentence is met.
HPS restricts itself to this specific type of pattern matching in order to avoid creating "false positive" links, which would frustrate the user. It will not attempt to create additional links to other databases, unless a publisher has requested broader attempts at linking. Generally, if additional links beyond NCBI's nucleotide are required, the vendor should then be using the appropriate
inter-ref tagging for all database links (and if this is a new approach for a particular journal, then your content developer should be notified of the change).
If there is a new external database that you would like to have link support for, please contact your content developer with an outline of the suggested change and information on the database.
Return to the HighWire DTD Vendor documentation
This information page created on 2.03.2003, updated 2.04.2004