BibClassify Admin Guide¶
1. Overview¶
BibClassify automatically extracts keywords from fulltext documents. The automatic assignment of keywords to textual documents has clear benefits in the digital library environment as it aids catalogization, classification and retrieval of documents.
1.1 Thesaurus¶
BibClassify performs an extraction of keywords based on the recurrence of specific terms, taken from a controlled vocabulary. A controlled vocabulary is a thesaurus of all the terms that are relevant in a specific context. When a context is defined by a discipline or branch of knowledge then the vocabulary is said to be a subject thesaurus. Various existing subject thesauri can be found here.
A subject thesaurus can be expressed in several different formats. Different institutions/disciplines have developed different ways of representing their vocabulary systems. The taxonomy used by bibclassify is expressed in RDF/SKOS. It allows not only to list keywords but to specify relations between the keywords and alternative ways to represent the same keyword.
<Concept rdf:about="http://cern.ch/thesauri/HEP.rdf#scalar"> <composite rdf:resource="http://cern.ch/thesauri/HEP.rdf#Composite.fieldtheoryscalar"/> <prefLabel xml:lang="en">scalar</prefLabel> <note xml:lang="en">nostandalone</note> </Concept> <Concept rdf:about="http://cern.ch/thesauri/HEP.rdf#fieldtheory"> <composite rdf:resource="http://cern.ch/thesauri/HEP.rdf#Composite.fieldtheoryscalar"/> <prefLabel xml:lang="en">field theory</prefLabel> <altLabel xml:lang="en">QFT</altLabel> <hiddenLabel xml:lang="en">/field theor\w*/</hiddenLabel> <note xml:lang="en">nostandalone</note> </Concept> <Concept rdf:about="http://cern.ch/thesauri/HEP.rdf#Composite.fieldtheoryscalar"> <compositeOf rdf:resource="http://cern.ch/thesauri/HEP.rdf#scalar"/> <compositeOf rdf:resource="http://cern.ch/thesauri/HEP.rdf#fieldtheory"/> <prefLabel xml:lang="en">field theory: scalar</prefLabel> <altLabel xml:lang="en">scalar field</altLabel> </Concept>
In RDF/SKOS, every keyword is wrapped around a concept which encapsulates the full semantics and hierarchical status of a term - including synonyms, alternative forms, broader concepts, notes and so on - rather than just a plain keyword.
The specification of the SKOS language and various manuals that aid the building of a semantic thesaurus can be found at the SKOS W3C website. Furthermore, BibClassify can function on top of an extended version of SKOS, which includes special elements such as key chains, composite keywords and special annotations. The extension of the SKOS language is documented in the hacking guide.
1.2 Keyword extraction¶
BibClassify computes the keywords of a fulltext document based on the frequency of thesaurus terms in it. In other words, it calculates how many times a thesaurus keyword (and its alternative and hidden labels, defined in the taxonomy) appears in a text and it ranks the results. Unlike other similar systems, BibClassify does not use any machine learning or AI methodologies - a just plain phrase matching using regular expressions: it exploits the conformation and richness of the thesaurus to produce accurate results. It is then clear that BibClassify performs best on top of rich, well-structured, subject thesauri expressed in the RDF/SKOS language.
A detailed account of the phrase matching mechanisms used by BibClassify is included in the hacking guide.
2. Running BibClassify¶
Dependencies. BibClassify requires Python RDFLib in order to process the RDF/SKOS taxonomy.
In order to extract relevant keywords from a document fulltext.pdf
based on a controlled vocabulary thesaurus.rdf, you would run
BibClassify as follows:
$ bibclassify.py -k thesaurus.rdf fulltext.pdf
Launching bibclassify --help shows the options available for
BibClassify:
Usage: bibclassify [OPTION]... [FILE/URL]...
bibclassify [OPTION]... [DIRECTORY]...
Searches keywords in FILEs and/or files in DIRECTORY(ies). If a directory is
specified, BibClassify will generate keywords for all PDF documents contained
in the directory. Can also run in a daemon mode, in which case the files to
be run are looked for from the database (=records modified since the last run).
General options:
-h, --help display this help and exit
-V, --version output version information and exit
-v, --verbose=LEVEL sets the verbose to LEVEL (=0)
-k, --taxonomy=NAME sets the taxonomy NAME. It can be a simple
controlled vocabulary or a descriptive RDF/SKOS
and can be located in a local file or URL.
Standalone file mode options:
-o, --output-mode=TYPE changes the output format to TYPE (text, marcxml or
html) (=text)
-s, --spires outputs keywords in the SPIRES format
-n, --keywords-number=INT sets the number of keywords displayed (=20), use 0
to set no limit
-m, --matching-mode=TYPE changes the search mode to TYPE (full or partial)
(=full)
--detect-author-keywords detect keywords that are explicitely written in the
document
Daemon mode options:
-i, --recid=RECID extract keywords for a record and store into DB
(=all necessary ones for pre-defined taxonomies)
-c, --collection=COLL extract keywords for a collection and store into DB
(=all necessary ones for pre-defined taxonomies)
Taxonomy management options:
--check-taxonomy checks the taxonomy and reports warnings and errors
--rebuild-cache ignores the existing cache and regenerates it
--no-cache don't cache the taxonomy
Backward compatibility options (discouraged):
-q equivalent to -s
-f FILE URL sets the file to read the keywords from
Examples (standalone file mode):
$ bibclassify -k HEP.rdf http://arxiv.org/pdf/0808.1825
$ bibclassify -k HEP.rdf article.pdf
$ bibclassify -k HEP.rdf directory/
Examples (daemon mode):
$ bibclassify -u admin -s 24h -L 23:00-05:00
$ bibclassify -u admin -i 1234
$ bibclassify -u admin -c Preprints
NB. BibClassify can run as a CDS Invenio module or as a standalone program. If you already run a server with a Invenio installation, you can simply run /opt/invenio/bin/bibclassify [options]. Otherwise, you can run from BibClassify sources bibclassify [options].
As an example, running BibClassify on document
nucl-th/0204033 using the
high-energy physics RDF/SKOS taxonomy (HEP.rdf) would yield the
following results (based on the HEP taxonomy from October 10th 2008):
Input file: 0204033.pdf
Author keywords:
Dense matter
Saturation
Unstable nuclei
Composite keywords:
10 nucleus: stability [36, 14]
6 saturation: density [25, 31]
6 energy: symmetry [35, 11]
4 nucleon: density [13, 31]
3 energy: Coulomb [35, 3]
2 energy: density [35, 31]
2 nuclear matter: asymmetry [21, 2]
1 n: matter [54, 36]
1 n: density [54, 31]
1 n: mass [54, 16]
Single keywords:
61 K0
23 equation of state
12 slope
4 mass number
4 nuclide
3 nuclear model
3 mass formula
2 charge distribution
2 elastic scattering
2 binding energy
or, the following keyword-cloud HTML visualization:
