Jekyll2026-10-06T09:51:02+00:00http://egonw.github.io/blog/feed/by_tag/beilstein.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenOscar4 command line utilities2010-11-18T00:00:00+00:002010-11-18T00:00:00+00:00http://egonw.github.io/blog/2010/11/18/oscar4-command-line-utilitiesOne goal of my three month project is to take Oscar4 to the community. We want to get it used more, and we need a larger development community. Oscar4 and the related technologies do a good, sometimes excellent, job, but have to be maintained, just like any other piece of code. To make using it easier, we are developing new APIs, as well as two user-oriented applications: a Taverna 2 plugin , and command line utilities. The Oscar4 Java API has slightly evolved in the last three weeks, removing some complexity. In this post, I will introduce the command line utilities.

Oscar4

Most people will be mostly interested into the full Oscar4 program, to extract chemical entities. Oscar3 was also capable of extracting data (like NMR spectra ), but that is not yet being ported. The OscarCLI program takes input, extracts chemicals, and where possible resolves them into connection tables (viz. InChI).

To extract chemicals from a line of text (e.g. “This is propane.”, you do:

$ java -cp oscar4-cli-4.0-SNAPSHOT.jar \
  uk.ac.cam.ch.wwmm.oscar.oscarcli.OscarCLI \
  This is propane.
propane: InChI=1/C3H8/c1-3-2/h3H2,1-2H3

For larger chunks of texts it is easier to route it via stdin, for which we can use the -stdin option:

$ echo "This is propane." | \
  java -cp oscar4-cli-4.0-SNAPSHOT.jar \
  uk.ac.cam.ch.wwmm.oscar.oscarcli.OscarCLI \
  -stdin
propane: InChI=1/C3H8/c1-3-2/h3H2,1-2H3

That way, we can easily process large plain text files (output omitted):

$ cat largeFile.txt | \
  java -cp oscar4-cli-4.0-SNAPSHOT.jar \
  uk.ac.cam.ch.wwmm.oscar.oscarcli.OscarCLI \
  -stdin

If you prefer RDF output, for further integration, use the -output text/turtle:

$ cat largeFile.txt | \
  java -cp oscar4-cli-4.0-SNAPSHOT.jar \
  uk.ac.cam.ch.wwmm.oscar.oscarcli.OscarCLI \
  -stdin -output text/turtle

This returns RDF using the CHEMINF ontology like:

@prefix dc:  .
@prefix rdfs:  .
@prefix ex:  .
@prefix cheminf:  .
@prefix sio: .

ex:entity0
  rdfs:subClassOf cheminf:CHEMINF_000000 ;
  dc:label "propane" ;
  cheminf:CHEMINF_000200 [
    a cheminf:CHEMINF_000113 ;
    sio:SIO_000300 "InChI=1/C3H8/c1-3-2/h3H2,1-2H3" .
  ] .

We can, however, also use Jericho to extract text from HTML pages, made available with the -html option, and pulling in a Beilstein Journal of Organic Chemistry paper with wget:

$ wget -qO- https://doi.org/10.3762/bjoc.6.122 | \
  java -cp oscar4-cli-4.0-SNAPSHOT.jar \
  uk.ac.cam.ch.wwmm.oscar.oscarcli.OscarCLI \
  -stdin -html

This will return 271 chemical entities recognized in the text, matching 48 unique chemical structures.

]]>Egon Willighagen