{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2010/11/18/oscar4-command-line-utilities.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/jsfck-t351", "url": "https://chem-bla-ics.linkedchemistry.info/2010/11/18/oscar4-command-line-utilities.html", "title": "Oscar4 command line utilities", "content_html": "

One goal of my three month project is to take Oscar4 to the community. We want to get it used more, and we need\na larger development community. Oscar4 and the related technologies do a good, sometimes excellent, job, but\nhave to be maintained, just like any other piece of code. To make using it easier, we are developing new APIs,\nas well as two user-oriented applications: a Taverna 2 plugin ,\nand command line utilities. The Oscar4 Java API \nhas slightly evolved in the last three weeks, removing some complexity. In this post, I will introduce the command\nline utilities.

\n\n

Oscar4

\n\n

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

\n\n

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

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

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

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

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

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

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

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

This returns RDF using the CHEMINF ontology like:

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

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

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

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

", "summary": "One 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.", "date_published": "2010-11-18T00:00:00+00:00", "date_modified": "2025-03-05T00:00:00+00:00", "tags": ["oscar","textmining","beilstein"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }