Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Newer
Older
100644 111 lines (110 sloc) 4.35 kb
92528c1 @cmungall init after moving from open-bio.org svn
authored
1 <page>
2 <title>Blipkit: Biomedical LogIc Programming Knowledge Integration Kit</title>
3 <section id="About Blip">
4 <p>
5 Blip is a collection of logic programming modules intended
6 primarily for bioinformatics and biomedical applications,
7 although it contains some modules which may be of more
8 general interest. Blip is intended to be both an application
9 library, and a deductive database/query system. Blip is
10 written in
11 <url to="SWI-Prolog"/>, a
12 fast, robust and scalable implementation of ISO Prolog.
13 </p>
14 <p>
15 Blip is <a href="http://www.fsf.org">Free Software</a>,
16 available, licensed under the <url to="LGPL"/>.
17 </p>
18 <p>Blip, aka <i>blipkit</i> can be cited as...</p>
19 </section>
20 <section id="Features">
21 <p>Here are some distinguishing characteristics of Blip</p>
22 <ul>
23 <li>
24 <b>Lightweight</b>. Bloat-free: Blip only has as many modules
25 as it needs to do its job.
26 </li>
27 <li>
28 <b>Fast</b>.
29 </li>
30 <li>
31 <b>Declarative</b>. Say <i>what</i> you want to do, not
32 <i>how</i> you want to do it
33 </li>
34 <li>
35 Blip can be <b>Query-oriented</b>: specify your data
36 sources and ask your query
37 </li>
38 <li>
39 Blip can be <b>Application-oriented</b>: it is designed to be
40 used as an application library used by other bioinformatics tools
41 </li>
42 <li>
43 Mature and fully functional <b>ontology module</b> for
44 handling both <url to="OBO"/>-style ontologies and <url
45 to="OWL"/> ontologies.
46 </li>
47 <li>
48 Modules for handling <b>biological sequences</b> and
49 <b>sequence features</b>. [currently limited functionality,
50 added as needed]
51 </li>
52 <li>
53 A <b>systems biology</b> module for querying pathway and
54 interaction data. [currently limited functionality, added as needed]
55 </li>
56 <li>
57 <b>Relational database integration</b>. SQL can be viewed as a
58 highly restricted dialect of Prolog. Although the SWI-Prolog
59 in-memory database is fast and scalable, sometimes it is nice
60 to be able to fetch data from an external database. Blip
61 contains a generic SQL utility module and predicate mappings
62 for the GO database, Ensembl and Chado
63 </li>
64 <li>
65 <b>Integration</b> with a variety of bioinformatics <b>file
66 formats</b>. SWI-Prolog has a variety of fast libraries for
67 dealing with XML, RDF and tabular data files. Blip provides
68 bridges from bio file formats encoded using these syntaxes
69 into its native models. For other syntaxes, Blip seamlessly
70 integrates other packages such as <url to="BioPerl"/> and <url
71 to="go-perl"/>. Although these dependencies require extra
72 installation, there is no point reinventing the wheel
73 </li>
74 <li>
75 <b>Rapid development of web applications</b>. Blip extends <url
76 to="SWI-Prolog"/>'s excellent http support with a simple and
77 powerful logical-functional-programming style application
78 server, <pageref page="serval"/>. This has been used to
79 prototype a fully-featured next-generation replacement for
80 the GO project <url to="amigo"/> browser.
81 </li>
82 <li>
83 <b>Scalable</b>. Blip is not intended to be a toy system on
84 toy data (although it is happy to be used as a toy if you
85 like!). It is intended to be used as an application component
86 and a tool operating on real-world biological and biomedical
87 data
88 </li>
89 <li>
90 It's <b>free!</b>
91 </li>
92 <li>
93 It's <b>fun!</b>
94 </li>
95 </ul>
96 </section>
97 <section id="News">
98 <news>
99 <newsitem date="2009-05-15">
100 <a href="http://blipkit.wordpress.com">Blip Blog</a> up
101 </newsitem>
102 </news>
103 </section>
104 <lastmod>
105 <!-- Created: Mon May 2 09:02:21 PDT 2005 -->
106 <!-- hhmts start -->
107 Last modified: Fri Sep 30 18:23:46 PDT 2005
108 <!-- hhmts end -->
109 </lastmod>
110 </page>
Something went wrong with that request. Please try again.