Initial submission of biosql ontology thoughts and files.

biosql_ontologies/18463287.rdf

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+<?xml version="1.0" encoding="UTF-8"?><rdf:RDF xmlns:bibtex="http://purl.oclc.org/NET/nkouf/ns/bibtex#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:pcv="http://prismstandard.org/namespaces/1.2/basic/" xmlns:prism="http://prismstandard.org/namespaces/1.2/basic/"><bibtex:Article rdf:about="info:pmid/"><dc:title>Identification of innate immunity genes and pathways using a comparative genomics approach.</dc:title><dcterms:abstract>To reveal regulators of innate immunity, we used RNAi assays to monitor the immune response when genes are inhibited in Caenorhabditis elegans and mouse macrophages. Genes that altered innate immune responsiveness in C. elegans were validated in murine macrophages, resulting in the discovery of 11 genes that regulate the innate immune response in both systems and the subsequent identification of a protein interaction network with a conserved role in innate immunity regulation. We confirmed the role of four of these 11 genes in antimicrobial gene regulation using available mutants in C. elegans. Several of these genes (acy-1, tub-2, and tbc-1) also regulate susceptibility to the pathogen Pseudomonas aeruginosa. These genes may prove critical to understanding host defense and represent potential therapeutic targets for infectious and immunological diseases.</dcterms:abstract><dcterms:creator>Scott Alper,</dcterms:creator><dcterms:creator>Rebecca Laws,</dcterms:creator><dcterms:creator>Brad Lackford,</dcterms:creator><dcterms:creator>Windy A Boyd,</dcterms:creator><dcterms:creator>Paul Dunlap,</dcterms:creator><dcterms:creator>Jonathan H Freedman,</dcterms:creator><dcterms:creator>David A Schwartz,</dcterms:creator><prism:publicationName>Proc Natl Acad Sci U S A</prism:publicationName><prism:publicationDate>2008-May-13</prism:publicationDate><prism:volume>105</prism:volume><prism:startingPage>7016</prism:startingPage><prism:endingPage>-21</prism:endingPage><prism:isPartOf>urn:issn:1091-6490</prism:isPartOf><pcv:relatedTerm>tub-2</pcv:relatedTerm><pcv:relatedTerm>acy-1</pcv:relatedTerm><pcv:relatedTerm>tbc-1</pcv:relatedTerm><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/><pcv:relatedTerm/></bibtex:Article></rdf:RDF>

biosql_ontologies/GenBank_General.dtd

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+<!-- ============================================
+     ::DATATOOL:: Generated from "seqblock.asn"
+     ::DATATOOL:: by application DATATOOL version 1.5.0
+     ::DATATOOL:: on 06/06/2006 23:03:48
+     ============================================ -->
+
+<!-- GenBank_General.dtd
+  This file is built from a series of basic modules.
+  The actual ELEMENT and ENTITY declarations are in the modules.
+  This file is used to put them together.
+-->
+
+<!ENTITY % NCBI_Entity_module PUBLIC "-//NCBI//NCBI Entity Module//EN" "NCBI_Entity.mod.dtd">
+%NCBI_Entity_module;
+
+<!ENTITY % GenBank_General_module PUBLIC "-//NCBI//GenBank General Module//EN" "GenBank_General.mod.dtd">
+%GenBank_General_module;
+
+<!ENTITY % NCBI_General_module PUBLIC "-//NCBI//NCBI General Module//EN" "NCBI_General.mod.dtd">
+%NCBI_General_module;

biosql_ontologies/GenBank_General.mod.dtd

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+<!-- ============================================
+     ::DATATOOL:: Generated from "seqblock.asn"
+     ::DATATOOL:: by application DATATOOL version 1.9.0
+     ::DATATOOL:: on 04/10/2008 16:04:22
+     ============================================ -->
+
+<!-- ============================================ -->
+<!-- This section is mapped from module "GenBank-General"
+================================================= -->
+
+<!--
+*********************************************************************
+
+  GenBank specific data
+  This block of specifications was developed by Jim Ostell of
+      NCBI
+
+*********************************************************************
+-->
+
+<!-- Elements used by other modules:
+          GB-block -->
+
+<!-- Elements referenced from other modules:
+          Date FROM NCBI-General -->
+<!-- ============================================ -->
+
+<!-- GenBank specific descriptions -->
+<!ELEMENT GB-block (
+        GB-block_extra-accessions?, 
+        GB-block_source?, 
+        GB-block_keywords?, 
+        GB-block_origin?, 
+        GB-block_date?, 
+        GB-block_entry-date?, 
+        GB-block_div?, 
+        GB-block_taxonomy?)>
+
+<!ELEMENT GB-block_extra-accessions (GB-block_extra-accessions_E*)>
+
+
+<!ELEMENT GB-block_extra-accessions_E (#PCDATA)>
+
+<!-- source line -->
+<!ELEMENT GB-block_source (#PCDATA)>
+
+<!ELEMENT GB-block_keywords (GB-block_keywords_E*)>
+
+
+<!ELEMENT GB-block_keywords_E (#PCDATA)>
+
+<!ELEMENT GB-block_origin (#PCDATA)>
+
+<!-- OBSOLETE old form Entry Date -->
+<!ELEMENT GB-block_date (#PCDATA)>
+
+<!-- replaces date -->
+<!ELEMENT GB-block_entry-date (Date)>
+
+<!-- GenBank division -->
+<!ELEMENT GB-block_div (#PCDATA)>
+
+<!-- continuation line of organism -->
+<!ELEMENT GB-block_taxonomy (#PCDATA)>
+