[Sbfc-svn] SF.net SVN: sbfc:[725] trunk

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Revision: 725
          http://sourceforge.net/p/sbfc/code/725
Author:   niko-rodrigue
Date:     2018-05-23 12:55:17 +0000 (Wed, 23 May 2018)
Log Message:
-----------
updated identifiers.org registry xml. Added javadoc to ConversionException.

Modified Paths:
--------------
    trunk/miriam.xml
    trunk/src/org/sbfc/converter/exceptions/ConversionException.java

Modified: trunk/miriam.xml
===================================================================

--- trunk/miriam.xml	2018-05-23 12:50:27 UTC (rev 724)
+++ trunk/miriam.xml	2018-05-23 12:55:17 UTC (rev 725)
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <!-- Export of Identifiers.org's Registry (full) -->
-<!-- Generated: Wed, 26 Jul 2017 14:17:31 GMT     -->
+<!-- Generated: Mon, 19 Mar 2018 14:06:44 GMT     -->
 <!-- http://identifiers.org/registry/            -->
 
-<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="Wed, 26 Jul 2017 14:17:31 GMT" data-version="Fri, 21 Jul 2017 09:49:14 GMT">
+<miriam xmlns="http://www.biomodels.net/MIRIAM/" date="Mon, 19 Mar 2018 14:06:44 GMT" data-version="Tue, 13 Mar 2018 11:08:28 GMT">
 	<datatype id="MIR:00000001" pattern="^\d+$" restricted="true" obsolete="true" replacement="MIR:00000010">
 		<comment>BIND doesn&apos;t exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available.</comment>
 		<name>BIND</name>
@@ -86,7 +86,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100565" state="up" reliability="93">
+			<resource id="MIR:00100565" state="down" reliability="94">
 				<dataResource>http://bioportal.bioontology.org/ontologies/CHEBI</dataResource>
 				<dataEntityExample>CHEBI:36927</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/CHEBI/$id</dataEntry>
@@ -110,7 +110,7 @@
 		</annotation>
 	</datatype>
 
-	<datatype id="MIR:00000003" pattern="^((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" restricted="true">
+	<datatype id="MIR:00000003" pattern="^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$" restricted="true">
 		<name>Ensembl</name>
 		<definition>Ensembl is a joint project between EMBL - EBI and the Sanger Institute  to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.</definition>
 		<uris>
@@ -169,6 +169,7 @@
 			<tag>eukaryotic</tag>
 			<tag>genome</tag>
 			<tag>nucleotide</tag>
+			<tag>schema.org</tag>
 			<tag>sequence</tag>
 		</tags>
 		<annotation>
@@ -218,7 +219,7 @@
 				<dataInstitution>Kyoto University Bioinformatics Center</dataInstitution>
 				<dataLocation>Japan</dataLocation>
 			</resource>
-			<resource id="MIR:00100003" state="up" reliability="99">
+			<resource id="MIR:00100003" state="down" reliability="97">
 				<dataResource>http://enzyme.expasy.org/</dataResource>
 				<dataEntityExample>1.1.1.1</dataEntityExample>
 				<dataEntry>http://enzyme.expasy.org/EC/$id</dataEntry>
@@ -234,6 +235,14 @@
 				<dataInstitution>Trinity College, Dublin</dataInstitution>
 				<dataLocation>Ireland</dataLocation>
 			</resource>
+			<resource id="MIR:00100835" state="unknown" reliability="0">
+				<dataResource>https://www.ebi.ac.uk/enzymeportal</dataResource>
+				<dataEntityExample>1.1.1.1</dataEntityExample>
+				<dataEntry>https://www.ebi.ac.uk/enzymeportal/search/ec/$id</dataEntry>
+				<dataInfo>Enzyme Portal through EMBL-EBI</dataInfo>
+				<dataInstitution>Enzyme Portal at European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
+				<dataLocation>UK</dataLocation>
+			</resource>
 		</resources>
 		<tags>
 			<tag>classification</tag>
@@ -402,7 +411,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100507" state="up" reliability="83">
+			<resource id="MIR:00100507" state="down" reliability="85">
 				<dataResource>http://bioportal.bioontology.org/ontologies/NCBITAXON</dataResource>
 				<dataEntityExample>9606</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/NCBITAXON/$id</dataEntry>
@@ -410,7 +419,7 @@
 				<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100695" state="up" reliability="95">
+			<resource id="MIR:00100695" state="down" reliability="85">
 				<dataResource>http://taxonomy.bio2rdf.org/fct/</dataResource>
 				<dataEntityExample>9606</dataEntityExample>
 				<dataEntry>http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:$id</dataEntry>
@@ -418,7 +427,7 @@
 				<dataInstitution>Bio2RDF.org</dataInstitution>
 				<dataLocation></dataLocation>
 			</resource>
-			<resource id="MIR:00100770" state="up" reliability="98">
+			<resource id="MIR:00100770" state="up" reliability="99">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/</dataResource>
 				<dataEntityExample>9606</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?short_form=NCBITaxon_$id</dataEntry>
@@ -470,7 +479,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100107" state="up" reliability="81">
+			<resource id="MIR:00100107" state="up" reliability="82">
 				<dataResource>http://biomodels.caltech.edu/</dataResource>
 				<dataEntityExample>BIOMD0000000048</dataEntityExample>
 				<dataEntry>http://biomodels.caltech.edu/$id</dataEntry>
@@ -478,7 +487,7 @@
 				<dataInstitution>California Institute of Technology</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100674" state="down" reliability="41">
+			<resource id="MIR:00100674" state="down" reliability="34">
 				<dataResource>http://cu.biomodels.bio2rdf.org/fct/</dataResource>
 				<dataEntityExample>BIOMD0000000048</dataEntityExample>
 				<dataEntry>http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id</dataEntry>
@@ -486,6 +495,14 @@
 				<dataInstitution>Bio2RDF.org</dataInstitution>
 				<dataLocation></dataLocation>
 			</resource>
+			<resource id="MIR:00100855" state="unknown" reliability="0">
+				<dataResource>https://www.omicsdi.org/</dataResource>
+				<dataEntityExample>BIOMD0000000048</dataEntityExample>
+				<dataEntry>https://www.omicsdi.org/dataset/biomodels/$id</dataEntry>
+				<dataInfo>BioModels through OmicsDI</dataInfo>
+				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
+				<dataLocation>UK</dataLocation>
+			</resource>
 		</resources>
 		<tags>
 			<tag>model</tag>
@@ -531,6 +548,7 @@
 		</resources>
 		<tags>
 			<tag>registry</tag>
+			<tag>schema.org</tag>
 		</tags>
 	</datatype>
 
@@ -558,6 +576,7 @@
 		</resources>
 		<tags>
 			<tag>disease</tag>
+			<tag>schema.org</tag>
 			<tag>taxonomy</tag>
 		</tags>
 		<annotation>
@@ -630,7 +649,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100697" state="down" reliability="30">
+			<resource id="MIR:00100697" state="down" reliability="24">
 				<dataResource>http://interpro.bio2rdf.org/fct/</dataResource>
 				<dataEntityExample>IPR000100</dataEntityExample>
 				<dataEntry>http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$id</dataEntry>
@@ -812,7 +831,7 @@
 				<dataInstitution>Europe PubMed Central partners</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100702" state="down" reliability="17">
+			<resource id="MIR:00100702" state="down" reliability="13">
 				<dataResource>http://pubmed.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>23735196</dataEntityExample>
 				<dataEntry>http://pubmed.bio2rdf.org/describe/?url=http://bio2rdf.org/pubmed:$id</dataEntry>
@@ -820,7 +839,7 @@
 				<dataInstitution>Bio2RDF.org</dataInstitution>
 				<dataLocation></dataLocation>
 			</resource>
-			<resource id="MIR:00100745" state="down" reliability="90">
+			<resource id="MIR:00100745" state="up" reliability="87">
 				<dataResource>http://linkedlifedata.com/</dataResource>
 				<dataEntityExample>23735196</dataEntityExample>
 				<dataEntry>http://linkedlifedata.com/resource/pubmed/id/$id</dataEntry>
@@ -855,6 +874,7 @@
 		</resources>
 		<tags>
 			<tag>bibliography</tag>
+			<tag>schema.org</tag>
 		</tags>
 		<annotation>
 			<format name="SBML">
@@ -895,7 +915,7 @@
 				<dataInstitution>Johns Hopkins University, Baltimore, Maryland</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100694" state="up" reliability="95">
+			<resource id="MIR:00100694" state="down" reliability="86">
 				<dataResource>http://omim.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>603903</dataEntityExample>
 				<dataEntry>http://omim.bio2rdf.org/describe/?url=http://bio2rdf.org/omim:$id</dataEntry>
@@ -1012,6 +1032,7 @@
 			<tag>human</tag>
 			<tag>pathway</tag>
 			<tag>reaction</tag>
+			<tag>schema.org</tag>
 		</tags>
 		<annotation>
 			<format name="SBML">
@@ -1039,7 +1060,7 @@
 		</uris>
 		<namespace>doi</namespace>
 		<resources>
-			<resource id="MIR:00100010" state="up" reliability="99" primary="true">
+			<resource id="MIR:00100010" state="down" reliability="95" primary="true">
 				<dataResource>http://www.doi.org/</dataResource>
 				<dataEntityExample>10.1038/nbt1156</dataEntityExample>
 				<dataEntry>http://doi.org/$id</dataEntry>
@@ -1047,7 +1068,7 @@
 				<dataInstitution>International DOI Foundation</dataInstitution>
 				<dataLocation>United Kingdom</dataLocation>
 			</resource>
-			<resource id="MIR:00100065" state="up" reliability="99">
+			<resource id="MIR:00100065" obsolete="true">
 				<dataResource>http://www.handle.net/index.html</dataResource>
 				<dataEntityExample>10.1038/nbt1156</dataEntityExample>
 				<dataEntry>http://hdl.handle.net/$id</dataEntry>
@@ -1055,7 +1076,7 @@
 				<dataInstitution>Corporation for National Research Initiatives</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100751" state="up" reliability="93">
+			<resource id="MIR:00100751" obsolete="true">
 				<dataResource>http://doai.io/</dataResource>
 				<dataEntityExample>10.1038/nbt1156</dataEntityExample>
 				<dataEntry>http://doai.io/$id</dataEntry>
@@ -1120,7 +1141,7 @@
 				<dataInstitution>Weizmann Institute of Science</dataInstitution>
 				<dataLocation>Israel</dataLocation>
 			</resource>
-			<resource id="MIR:00100165" state="down" reliability="98">
+			<resource id="MIR:00100165" state="up" reliability="95">
 				<dataResource>http://www.pdbj.org/</dataResource>
 				<dataEntityExample>2gc4</dataEntityExample>
 				<dataEntry>http://pdbj.org/mine/summary/$id</dataEntry>
@@ -1208,7 +1229,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:10802651</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100012" state="up" reliability="99">
+			<resource id="MIR:00100012" state="down" reliability="92">
 				<dataResource>http://www.ebi.ac.uk/QuickGO/</dataResource>
 				<dataEntityExample>GO:0006915</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/QuickGO/GTerm?id=$id</dataEntry>
@@ -1224,7 +1245,7 @@
 				<dataInstitution>The Gene Ontology Consortium</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100015" state="down" reliability="96">
+			<resource id="MIR:00100015" state="down" reliability="90">
 				<dataResource>http://www.informatics.jax.org/searches/GO_form.shtml</dataResource>
 				<dataEntityExample>GO:0006915</dataEntityExample>
 				<dataEntry>http://www.informatics.jax.org/searches/GO.cgi?id=$id</dataEntry>
@@ -1232,7 +1253,7 @@
 				<dataInstitution>The Jackson Laboratory</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100237" state="up" reliability="95">
+			<resource id="MIR:00100237" state="down" reliability="95">
 				<dataResource>http://bioportal.bioontology.org/ontologies/GO</dataResource>
 				<dataEntityExample>GO:0006915</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/GO/$id</dataEntry>
@@ -1308,17 +1329,17 @@
 			<documentation type="PMID">urn:miriam:pubmed:14681421</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100033" state="up" reliability="99" primary="true">
+			<resource id="MIR:00100033" state="down" reliability="94" primary="true">
 				<dataResource>http://www.yeastgenome.org/</dataResource>
-				<dataEntityExample>S000028457</dataEntityExample>
+				<dataEntityExample>S000003909</dataEntityExample>
 				<dataEntry>http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=$id</dataEntry>
 				<dataInfo>SGD</dataInfo>
 				<dataInstitution>Stanford University</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100703" state="up" reliability="95">
+			<resource id="MIR:00100703" state="down" reliability="85">
 				<dataResource>http://sgd.bio2rdf.org/fct</dataResource>
-				<dataEntityExample>S000006169</dataEntityExample>
+				<dataEntityExample>S000003909</dataEntityExample>
 				<dataEntry>http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$id</dataEntry>
 				<dataInfo>Bio2RDF</dataInfo>
 				<dataInstitution>Bio2RDF.org</dataInstitution>
@@ -1355,8 +1376,6 @@
 		<uris>
 			<uri type="URN">urn:miriam:sbo</uri>
 			<uri type="URL">http://identifiers.org/sbo/</uri>
-			<uri type="URL" deprecated="true">http://identifiers.org/biomodels.sbo/</uri>
-			<uri type="URL" deprecated="true">http://identifiers.org/obo.sbo/</uri>
 			<uri type="URN" deprecated="true">urn:miriam:biomodels.sbo</uri>
 			<uri type="URN" deprecated="true">urn:miriam:obo.sbo</uri>
 			<uri type="URL" deprecated="true">http://www.biomodels.net/SBO/</uri>
@@ -1383,7 +1402,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100242" state="down" reliability="90">
+			<resource id="MIR:00100242" state="down" reliability="88">
 				<dataResource>http://bioportal.bioontology.org/ontologies/SBO</dataResource>
 				<dataEntityExample>SBO:0000262</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/SBO/$id</dataEntry>
@@ -1518,7 +1537,7 @@
 				<dataInstitution>Cold Spring Harbor Laboratory</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100704" state="up" reliability="96">
+			<resource id="MIR:00100704" state="down" reliability="85">
 				<dataResource>http://wormbase.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>WBGene00000001</dataEntityExample>
 				<dataEntry>http://wormbase.bio2rdf.org/describe/?url=http://bio2rdf.org/wormbase:$id</dataEntry>
@@ -1696,7 +1715,7 @@
 				<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100066" state="down" reliability="97">
+			<resource id="MIR:00100066" state="up" reliability="97">
 				<dataResource>http://www.ddbj.nig.ac.jp/</dataResource>
 				<dataEntityExample>X58356</dataEntityExample>
 				<dataEntry>http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&amp;accession_number=$id</dataEntry>
@@ -1858,7 +1877,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:16381852</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100056" state="up" reliability="99">
+			<resource id="MIR:00100056" state="down" reliability="97">
 				<dataResource>http://www.expasy.org/prosite/</dataResource>
 				<dataEntityExample>PS00001</dataEntityExample>
 				<dataEntry>http://prosite.expasy.org/$id</dataEntry>
@@ -1944,7 +1963,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:17170002</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100059" state="up" reliability="98">
+			<resource id="MIR:00100059" state="up" reliability="99">
 				<dataResource>http://pubchem.ncbi.nlm.nih.gov/</dataResource>
 				<dataEntityExample>100101</dataEntityExample>
 				<dataEntry>http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$id</dataEntry>
@@ -2013,7 +2032,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12519949</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100061" state="probably up" reliability="100">
+			<resource id="MIR:00100061" state="probably up" reliability="100" primary="true">
 				<dataResource>http://www.ebi.ac.uk/arrayexpress/</dataResource>
 				<dataEntityExample>E-MEXP-1712</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/arrayexpress/experiments/$id</dataEntry>
@@ -2021,6 +2040,14 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
+			<resource id="MIR:00100854" state="unknown" reliability="0">
+				<dataResource>https://www.omicsdi.org/</dataResource>
+				<dataEntityExample>E-MEXP-1712</dataEntityExample>
+				<dataEntry>https://www.omicsdi.org/dataset/arrayexpress-repository/$id</dataEntry>
+				<dataInfo>ArrayExpress through OmicsDI</dataInfo>
+				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
+				<dataLocation>UK</dataLocation>
+			</resource>
 		</resources>
 		<tags>
 			<tag>expression</tag>
@@ -2133,7 +2160,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:17130148</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100067" state="down" reliability="95">
+			<resource id="MIR:00100067" state="down" reliability="89">
 				<dataResource>http://www.ncbi.nlm.nih.gov/projects/RefSeq/</dataResource>
 				<dataEntityExample>NP_012345</dataEntityExample>
 				<dataEntry>http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id</dataEntry>
@@ -2157,7 +2184,7 @@
 		</annotation>
 	</datatype>
 
-	<datatype id="MIR:00000040" pattern="^\d+\.[A-Z]\.\d+\.\d+(\.\d+)?$">
+	<datatype id="MIR:00000040" pattern="^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$">
 		<name>Transport Classification Database</name>
 		<synonyms>
 			<synonym>TCDB</synonym>
@@ -2207,7 +2234,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:14681372</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100069" state="down" reliability="80">
+			<resource id="MIR:00100069" state="up" reliability="79">
 				<dataResource>http://www.ebi.ac.uk/uniparc/</dataResource>
 				<dataEntityExample>UPI000000000A</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&amp;id=$id</dataEntry>
@@ -2248,7 +2275,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:17135203</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100070" state="down" reliability="83">
+			<resource id="MIR:00100070" state="down" reliability="77">
 				<dataResource>http://mint.bio.uniroma2.it/mint/</dataResource>
 				<dataEntityExample>MINT-10000</dataEntityExample>
 				<dataEntry>http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id</dataEntry>
@@ -2256,7 +2283,7 @@
 				<dataInstitution>University of Rome Tor Vergata, Rome</dataInstitution>
 				<dataLocation>Italy</dataLocation>
 			</resource>
-			<resource id="MIR:00100654" state="up" reliability="91">
+			<resource id="MIR:00100654" state="up" reliability="92">
 				<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
 				<dataEntityExample>MINT-7905142</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/intact/query/interaction_id:$id</dataEntry>
@@ -2555,7 +2582,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12444417</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100078" state="up" reliability="84">
+			<resource id="MIR:00100078" state="up" reliability="85">
 				<dataResource>http://arabidopsis.org/index.jsp</dataResource>
 				<dataEntityExample>AT1G01030</dataEntityExample>
 				<dataEntry>http://arabidopsis.org/servlets/TairObject?type=locus&amp;name=$id</dataEntry>
@@ -2578,7 +2605,7 @@
 		</annotation>
 	</datatype>
 
-	<datatype id="MIR:00000051" pattern="^HMDB\d{5}$">
+	<datatype id="MIR:00000051" pattern="^HMDB\d+$">
 		<name>HMDB</name>
 		<synonyms>
 			<synonym>Human Metabolome Database</synonym>
@@ -2669,7 +2696,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18451766</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100081" state="up" reliability="98">
+			<resource id="MIR:00100081" state="up" reliability="98" primary="true">
 				<dataResource>http://www.peptideatlas.org/</dataResource>
 				<dataEntityExample>PAp00000009</dataEntityExample>
 				<dataEntry>https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&amp;searchForThis=$id</dataEntry>
@@ -2691,7 +2718,7 @@
 		</annotation>
 	</datatype>
 
-	<datatype id="MIR:00000054" pattern="^GDS\d+$">
+	<datatype id="MIR:00000054" pattern="^G(PL|SM|SE|DS)\d+$">
 		<name>GEO</name>
 		<synonyms>
 			<synonym>Gene Expression Omnibus</synonym>
@@ -2706,10 +2733,10 @@
 			<documentation type="PMID">urn:miriam:pubmed:11752295</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100082" state="up" reliability="99">
+			<resource id="MIR:00100082" state="down" reliability="93">
 				<dataResource>http://www.ncbi.nlm.nih.gov/geo/</dataResource>
 				<dataEntityExample>GDS1234</dataEntityExample>
-				<dataEntry>http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=$id</dataEntry>
+				<dataEntry>https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$id</dataEntry>
 				<dataInfo>Gene Expression Omnibus at NCBI</dataInfo>
 				<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
 				<dataLocation>USA</dataLocation>
@@ -2739,7 +2766,7 @@
 			<documentation type="URL">http://www.geneontology.org/GO.evidence.shtml</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100083" state="down" reliability="89">
+			<resource id="MIR:00100083" state="down" reliability="82">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/eco</dataResource>
 				<dataEntityExample>ECO:0000006</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=$id</dataEntry>
@@ -2747,7 +2774,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100235" state="down" reliability="82">
+			<resource id="MIR:00100235" state="down" reliability="74">
 				<dataResource>http://bioportal.bioontology.org/ontologies/ECO</dataResource>
 				<dataEntityExample>ECO:0000006</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/ECO/$id</dataEntry>
@@ -2771,7 +2798,6 @@
 		<uris>
 			<uri type="URN">urn:miriam:mod</uri>
 			<uri type="URL">http://identifiers.org/mod/</uri>
-			<uri type="URL" deprecated="true">http://identifiers.org/psimod/</uri>
 			<uri type="URL" deprecated="true">http://identifiers.org/obo.psi-mod/</uri>
 			<uri type="URN" deprecated="true">urn:miriam:obo.psi-mod</uri>
 			<uri type="URN" deprecated="true">urn:miriam:psimod</uri>
@@ -2860,7 +2886,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:16381927</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100086" state="down" reliability="90">
+			<resource id="MIR:00100086" state="down" reliability="84">
 				<dataResource>http://thebiogrid.org/</dataResource>
 				<dataEntityExample>31623</dataEntityExample>
 				<dataEntry>http://thebiogrid.org/$id</dataEntry>
@@ -2895,7 +2921,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:17991683</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100087" state="down" reliability="97">
+			<resource id="MIR:00100087" state="down" reliability="90">
 				<dataResource>http://merops.sanger.ac.uk/index.htm</dataResource>
 				<dataEntityExample>S01.001</dataEntityExample>
 				<dataEntry>http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$id</dataEntry>
@@ -2930,7 +2956,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12952881</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100088" state="probably up" reliability="96">
+			<resource id="MIR:00100088" state="probably up" reliability="97">
 				<dataResource>http://www.pantherdb.org/</dataResource>
 				<dataEntityExample>PTHR12345</dataEntityExample>
 				<dataEntry>http://www.pantherdb.org/panther/family.do?clsAccession=$id</dataEntry>
@@ -2967,7 +2993,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:10592232</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100089" state="up" reliability="98">
+			<resource id="MIR:00100089" state="up" reliability="97">
 				<dataResource>http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/</dataResource>
 				<dataEntityExample>PR00001</dataEntityExample>
 				<dataEntry>http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&amp;display_opts=Prints&amp;category=None&amp;queryform=false&amp;regexpr=off</dataEntry>
@@ -3012,7 +3038,7 @@
 				<dataInstitution>Rutgers, The State University of New Jersey</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100615" state="up" reliability="98">
+			<resource id="MIR:00100615" state="up" reliability="97">
 				<dataResource>http://ligand-expo.rcsb.org/</dataResource>
 				<dataEntityExample>ABC</dataEntityExample>
 				<dataEntry>http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&amp;target=$id&amp;operation=ccid</dataEntry>
@@ -3079,7 +3105,7 @@
 			<documentation type="URL">http://www.worldcat.org/whatis/default.jsp</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100092" state="up" reliability="95">
+			<resource id="MIR:00100092" state="down" reliability="93">
 				<dataResource>http://isbndb.com/</dataResource>
 				<dataEntityExample>9781584885658</dataEntityExample>
 				<dataEntry>http://isbndb.com/search-all.html?kw=$id</dataEntry>
@@ -3087,7 +3113,7 @@
 				<dataInstitution>ISNBdb project, San Gabriel, California</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100093" state="down" reliability="94">
+			<resource id="MIR:00100093" state="down" reliability="88">
 				<dataResource>http://www.worldcat.org/</dataResource>
 				<dataEntityExample>9781584885658</dataEntityExample>
 				<dataEntry>http://www.worldcat.org/isbn/$id</dataEntry>
@@ -3126,7 +3152,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18428683</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100094" state="up" reliability="96" primary="true">
+			<resource id="MIR:00100094" state="up" reliability="97" primary="true">
 				<dataResource>http://www.ebi.ac.uk/pride/</dataResource>
 				<dataEntityExample>1</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/pride/archive/assays/$id</dataEntry>
@@ -3160,7 +3186,7 @@
 			<documentation type="URL">http://pubs.acs.org/doi/ipdf/10.1021/ci300309k</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100095" state="up" reliability="95">
+			<resource id="MIR:00100095" state="up" reliability="96">
 				<dataResource>http://www.3dmet.dna.affrc.go.jp/</dataResource>
 				<dataEntityExample>B00162</dataEntityExample>
 				<dataEntry>http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id</dataEntry>
@@ -3209,7 +3235,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100236" state="up" reliability="95">
+			<resource id="MIR:00100236" state="down" reliability="95">
 				<dataResource>http://bioportal.bioontology.org/ontologies/FMA</dataResource>
 				<dataEntityExample>FMA:67112</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/FMA_subset/$id</dataEntry>
@@ -3244,7 +3270,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19147664</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100098" state="up" reliability="93" primary="true">
+			<resource id="MIR:00100098" state="down" reliability="88" primary="true">
 				<dataResource>http://matrixdb.univ-lyon1.fr/</dataResource>
 				<dataEntityExample>P00747__P07355</dataEntityExample>
 				<dataEntry>http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&amp;value=$id&amp;class=Association</dataEntry>
@@ -3294,7 +3320,7 @@
 				<dataInstitution>National Center for Biotechnology Information (NCBI)</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100693" state="up" reliability="95">
+			<resource id="MIR:00100693" state="down" reliability="85">
 				<dataResource>http://ncbigene.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>100010</dataEntityExample>
 				<dataEntry>http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$id</dataEntry>
@@ -3509,7 +3535,7 @@
 			<documentation type="URL">http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100105" state="up" reliability="94">
+			<resource id="MIR:00100105" state="up" reliability="95">
 				<dataResource>http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp</dataResource>
 				<dataEntityExample>37</dataEntityExample>
 				<dataEntry>http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id</dataEntry>
@@ -3544,7 +3570,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18651794</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100106" state="up" reliability="99">
+			<resource id="MIR:00100106" state="down" reliability="94">
 				<dataResource>http://www.wikipathways.org/</dataResource>
 				<dataEntityExample>WP100</dataEntityExample>
 				<dataEntry>http://www.wikipathways.org/instance/$id</dataEntry>
@@ -3703,7 +3729,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100698" state="up" reliability="95">
+			<resource id="MIR:00100698" state="down" reliability="85">
 				<dataResource>http://hgnc.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>hgnc:2674</dataEntityExample>
 				<dataEntry>http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/$id</dataEntry>
@@ -3715,6 +3741,7 @@
 		<tags>
 			<tag>gene</tag>
 			<tag>human</tag>
+			<tag>schema.org</tag>
 		</tags>
 		<annotation>
 			<format name="SBML">
@@ -3743,7 +3770,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:15892872</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100112" state="up" reliability="99">
+			<resource id="MIR:00100112" state="up" reliability="96">
 				<dataResource>http://www.sequenceontology.org/</dataResource>
 				<dataEntityExample>SO:0000704</dataEntityExample>
 				<dataEntry>http://www.sequenceontology.org/miso/current_release/term/$id</dataEntry>
@@ -3751,7 +3778,7 @@
 				<dataInstitution>Department of Molecular and Cellular Biology, University of California, Berkeley</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100241" state="up" reliability="93">
+			<resource id="MIR:00100241" state="down" reliability="93">
 				<dataResource>http://bioportal.bioontology.org/ontologies/SO</dataResource>
 				<dataEntityExample>SO:0000704</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/SO/$id</dataEntry>
@@ -3827,7 +3854,7 @@
 			<documentation type="URL">http://precedings.nature.com/documents/3214/version/1</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100114" state="down" reliability="81">
+			<resource id="MIR:00100114" state="down" reliability="74">
 				<dataResource>http://www.grenoble.prabi.fr/obiwarehouse/unipathway</dataResource>
 				<dataEntityExample>UPA00206</dataEntityExample>
 				<dataEntry>http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id</dataEntry>
@@ -3879,7 +3906,7 @@
 				<dataInstitution>Maastricht University</dataInstitution>
 				<dataLocation>The Netherlands</dataLocation>
 			</resource>
-			<resource id="MIR:00100744" state="probably up" reliability="97">
+			<resource id="MIR:00100744" state="probably up" reliability="98">
 				<dataResource>https://www.ebi.ac.uk/rdf/services/chembl/</dataResource>
 				<dataEntityExample>CHEMBL308052</dataEntityExample>
 				<dataEntry>http://rdf.ebi.ac.uk/resource/chembl/molecule/$id</dataEntry>
@@ -3931,7 +3958,7 @@
 				<dataInstitution>Maastricht University</dataInstitution>
 				<dataLocation>The Netherlands</dataLocation>
 			</resource>
-			<resource id="MIR:00100743" state="probably up" reliability="97">
+			<resource id="MIR:00100743" state="probably up" reliability="98">
 				<dataResource>http://rdf.ebi.ac.uk/resource/chembl/</dataResource>
 				<dataEntityExample>CHEMBL3467</dataEntityExample>
 				<dataEntry>http://rdf.ebi.ac.uk/resource/chembl/target/$id</dataEntry>
@@ -4046,7 +4073,7 @@
 			<documentation type="URL">http://www.whocc.no/atc_ddd_publications/guidelines/</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100119" state="down" reliability="91">
+			<resource id="MIR:00100119" state="down" reliability="84">
 				<dataResource>http://www.whocc.no/atc_ddd_index/</dataResource>
 				<dataEntityExample>A10BA02</dataEntityExample>
 				<dataEntry>http://www.whocc.no/atc_ddd_index/?code=$id</dataEntry>
@@ -4082,7 +4109,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100120" state="up" reliability="86">
+			<resource id="MIR:00100120" state="down" reliability="80">
 				<dataResource>http://www.pharmgkb.org/</dataResource>
 				<dataEntityExample>PA146123006</dataEntityExample>
 				<dataEntry>http://www.pharmgkb.org/pathway/$id</dataEntry>
@@ -4116,7 +4143,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100121" state="up" reliability="86">
+			<resource id="MIR:00100121" state="down" reliability="80">
 				<dataResource>http://www.pharmgkb.org/</dataResource>
 				<dataEntityExample>PA447218</dataEntityExample>
 				<dataEntry>http://www.pharmgkb.org/disease/$id</dataEntry>
@@ -4156,7 +4183,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:22103613</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100122" state="up" reliability="85">
+			<resource id="MIR:00100122" state="down" reliability="80">
 				<dataResource>http://www.pharmgkb.org/</dataResource>
 				<dataEntityExample>PA448710</dataEntityExample>
 				<dataEntry>http://www.pharmgkb.org/drug/$id</dataEntry>
@@ -4193,7 +4220,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:24265219</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100123" state="up" reliability="88">
+			<resource id="MIR:00100123" state="up" reliability="89">
 				<dataResource>http://bidd.nus.edu.sg/group/ttd/ttd.asp</dataResource>
 				<dataEntityExample>DAP000773</dataEntityExample>
 				<dataEntry>http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$id</dataEntry>
@@ -4228,7 +4255,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:24265219</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100124" state="up" reliability="89">
+			<resource id="MIR:00100124" state="up" reliability="90">
 				<dataResource>http://bidd.nus.edu.sg/group/ttd/ttd.asp</dataResource>
 				<dataEntityExample>TTDS00056</dataEntityExample>
 				<dataEntry>http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$id</dataEntry>
@@ -4262,7 +4289,7 @@
 			<documentation type="URL">http://senselab.med.yale.edu/NeuronDB/default.asp</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100125" state="down" reliability="92">
+			<resource id="MIR:00100125" state="down" reliability="84">
 				<dataResource>http://senselab.med.yale.edu/NeuronDB/</dataResource>
 				<dataEntityExample>265</dataEntityExample>
 				<dataEntry>http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id</dataEntry>
@@ -4541,7 +4568,7 @@
 				<dataInstitution>Departments of Computing Science &amp; Biological Sciences,  University of Alberta</dataInstitution>
 				<dataLocation>Canada</dataLocation>
 			</resource>
-			<resource id="MIR:00100691" state="up" reliability="96">
+			<resource id="MIR:00100691" state="down" reliability="86">
 				<dataResource>http://drugbank.bio2rdf.org/fct/</dataResource>
 				<dataEntityExample>DB00001</dataEntityExample>
 				<dataEntry>http://drugbank.bio2rdf.org/describe/?url=http://bio2rdf.org/drugbank:$id</dataEntry>
@@ -4617,7 +4644,7 @@
 			<documentation type="URL">http://www.smpdb.ca/</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100137" state="up" reliability="91">
+			<resource id="MIR:00100137" state="up" reliability="90">
 				<dataResource>http://www.smpdb.ca/pathways</dataResource>
 				<dataEntityExample>SMP00001</dataEntityExample>
 				<dataEntry>http://smpdb.ca/view/$id</dataEntry>
@@ -4658,7 +4685,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12478304</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100138" state="up" reliability="99">
+			<resource id="MIR:00100138" state="down" reliability="97">
 				<dataResource>http://www.phosphosite.org/homeAction.do</dataResource>
 				<dataEntityExample>12300</dataEntityExample>
 				<dataEntry>http://www.phosphosite.org/proteinAction.do?id=$id</dataEntry>
@@ -4727,7 +4754,7 @@
 			<documentation type="URL">http://teddyontology.sourceforge.net/</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100140" state="up" reliability="94">
+			<resource id="MIR:00100140" state="down" reliability="95">
 				<dataResource>http://teddyontology.sourceforge.net/</dataResource>
 				<dataEntityExample>TEDDY_0000066</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/TEDDY/$id</dataEntry>
@@ -4735,7 +4762,7 @@
 				<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100761" state="up" reliability="98">
+			<resource id="MIR:00100761" state="up" reliability="99">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/teddy</dataResource>
 				<dataEntityExample>TEDDY_0000066</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/teddy/terms?short_form=$id</dataEntry>
@@ -4764,7 +4791,7 @@
 			<documentation type="URL">http://www.ebi.ac.uk/compneur-srv/kisao/</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100141" state="up" reliability="97">
+			<resource id="MIR:00100141" state="down" reliability="96">
 				<dataResource>http://bioportal.bioontology.org/ontologies/KISAO</dataResource>
 				<dataEntityExample>KISAO_0000057</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/KISAO/kisao:$id</dataEntry>
@@ -4772,7 +4799,7 @@
 				<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100757" state="up" reliability="98">
+			<resource id="MIR:00100757" state="up" reliability="99">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/kisao</dataResource>
 				<dataEntityExample>KISAO_0000057</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/kisao/terms?short_form=$id</dataEntry>
@@ -4864,7 +4891,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100234" state="up" reliability="95">
+			<resource id="MIR:00100234" state="down" reliability="95">
 				<dataResource>http://bioportal.bioontology.org/ontologies/CL</dataResource>
 				<dataEntityExample>CL:0000232</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/CL/$id</dataEntry>
@@ -4912,7 +4939,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100233" state="up" reliability="95">
+			<resource id="MIR:00100233" state="down" reliability="95">
 				<dataResource>http://bioportal.bioontology.org/ontologies/BTO</dataResource>
 				<dataEntityExample>BTO:0000146</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/BTO/$id</dataEntry>
@@ -4959,7 +4986,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100238" state="up" reliability="95">
+			<resource id="MIR:00100238" state="down" reliability="95">
 				<dataResource>http://bioportal.bioontology.org/ontologies/PATO</dataResource>
 				<dataEntityExample>PATO:0001998</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/PATO/$id</dataEntry>
@@ -5033,7 +5060,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19759275</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100147" state="down" reliability="94">
+			<resource id="MIR:00100147" state="down" reliability="86">
 				<dataResource>http://www.glycome-db.org/showMenu.action?major=database</dataResource>
 				<dataEntityExample>1</dataEntityExample>
 				<dataEntry>http://www.glycome-db.org/database/showStructure.action?glycomeId=$id</dataEntry>
@@ -5137,7 +5164,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:15608179</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100150" state="up" reliability="94">
+			<resource id="MIR:00100150" state="up" reliability="93">
 				<dataResource>http://prodom.prabi.fr/prodom/current/html/home.php</dataResource>
 				<dataEntityExample>PD10000</dataEntityExample>
 				<dataEntry>http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&amp;query=$id</dataEntry>
@@ -5245,7 +5272,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:15892874</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100764" state="up" reliability="98">
+			<resource id="MIR:00100764" state="up" reliability="97">
 				<dataResource>http://obofoundry.org/ontology/ro.html</dataResource>
 				<dataEntityExample>RO_0002533</dataEntityExample>
 				<dataEntry>http://purl.obolibrary.org/obo/$id</dataEntry>
@@ -5253,7 +5280,7 @@
 				<dataInstitution>University of Michigan Medical School (MI), Lawrence Berkeley National Laboratory (CA) and Science Commons (MA)</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100767" state="up" reliability="98">
+			<resource id="MIR:00100767" state="up" reliability="99">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/ro</dataResource>
 				<dataEntityExample>RO_0002533</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/ro/terms?short_form=$id</dataEntry>
@@ -5326,7 +5353,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:17893861</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100155" state="up" reliability="95">
+			<resource id="MIR:00100155" state="up" reliability="96">
 				<dataResource>http://www.imexconsortium.org/</dataResource>
 				<dataEntityExample>IM-19210-3</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id</dataEntry>
@@ -5334,7 +5361,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100663" state="up" reliability="96">
+			<resource id="MIR:00100663" state="up" reliability="97">
 				<dataResource>http://www.ebi.ac.uk/intact/</dataResource>
 				<dataEntityExample>IM-19210-3</dataEntityExample>
 				<dataEntry>https://imexcentral.org/icentral/imex/rec/$id</dataEntry>
@@ -5369,7 +5396,7 @@
 			<documentation type="URL">http://irefindex.uio.no/wiki/iRefIndex</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100156" state="up" reliability="97">
+			<resource id="MIR:00100156" state="up" reliability="98">
 				<dataResource>http://wodaklab.org/iRefWeb/</dataResource>
 				<dataEntityExample>617102</dataEntityExample>
 				<dataEntry>http://wodaklab.org/iRefWeb/interaction/show/$id</dataEntry>
@@ -5406,7 +5433,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18556668</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100157" state="down" reliability="94">
+			<resource id="MIR:00100157" state="down" reliability="86">
 				<dataResource>http://www.jcvi.org/mpidb/about.php</dataResource>
 				<dataEntityExample>172</dataEntityExample>
 				<dataEntry>http://www.jcvi.org/mpidb/experiment.php?interaction_id=$id</dataEntry>
@@ -5476,7 +5503,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18975148</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100160" state="up" reliability="95" primary="true">
+			<resource id="MIR:00100160" state="down" reliability="92" primary="true">
 				<dataResource>http://www.neurolex.org/wiki/Main_Page</dataResource>
 				<dataEntityExample>Birnlex_721</dataEntityExample>
 				<dataEntry>http://www.neurolex.org/wiki/$id</dataEntry>
@@ -5484,7 +5511,7 @@
 				<dataInstitution>Department of Neuroscience, University of California, San Diego</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100183" state="up" reliability="97">
+			<resource id="MIR:00100183" state="down" reliability="97">
 				<dataResource>http://bioportal.bioontology.org/ontologies/BIRNLEX</dataResource>
 				<dataEntityExample>birnlex_1672</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/BIRNLEX/$id</dataEntry>
@@ -5533,7 +5560,7 @@
 				<dataInstitution>University of Michigan Medical School (MI), awrence Berkeley National Laboratory (CA) and Science Commons (MA)</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100177" state="probably up" reliability="65">
+			<resource id="MIR:00100177" state="down" reliability="68">
 				<dataResource>http://bioportal.bioontology.org/ontologies/OBI</dataResource>
 				<dataEntityExample>OBI:0000070</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/OBI/$id</dataEntry>
@@ -5541,7 +5568,7 @@
 				<dataInstitution>National Center for Biomedical Ontology, Stanford</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100760" state="up" reliability="98">
+			<resource id="MIR:00100760" state="up" reliability="99">
 				<dataResource>http://www.ebi.ac.uk/ols/ontologies/obi</dataResource>
 				<dataEntityExample>OBI:0000070</dataEntityExample>
 				<dataEntry>http://www.ebi.ac.uk/ols/ontologies/obi/terms?obo_id=$id</dataEntry>
@@ -5626,7 +5653,7 @@
 			<documentation type="URL">http://sig.biostr.washington.edu/projects/biosim/opb-intro.html</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100167" state="down" reliability="68">
+			<resource id="MIR:00100167" state="down" reliability="62">
 				<dataResource>http://bioportal.bioontology.org/ontologies/OPB</dataResource>
 				<dataEntityExample>OPB_00573</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$id</dataEntry>
@@ -5663,7 +5690,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:15072998</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100168" state="up" reliability="94">
+			<resource id="MIR:00100168" state="up" reliability="95">
 				<dataResource>http://jjj.biochem.sun.ac.za/models/</dataResource>
 				<dataEntityExample>curien</dataEntityExample>
 				<dataEntry>http://jjj.biochem.sun.ac.za/models/$id/</dataEntry>
@@ -5671,7 +5698,7 @@
 				<dataInstitution>Department of Biochemistry, Stellenbosch University</dataInstitution>
 				<dataLocation>South Africa</dataLocation>
 			</resource>
-			<resource id="MIR:00100169" state="down" reliability="79">
+			<resource id="MIR:00100169" state="down" reliability="72">
 				<dataResource>http://jjj.bio.vu.nl/models/</dataResource>
 				<dataEntityExample>curien</dataEntityExample>
 				<dataEntry>http://jjj.bio.vu.nl/models/$id/</dataEntry>
@@ -5679,7 +5706,7 @@
 				<dataInstitution>University of Amsterdam</dataInstitution>
 				<dataLocation>Netherlands</dataLocation>
 			</resource>
-			<resource id="MIR:00100170" state="up" reliability="73">
+			<resource id="MIR:00100170" state="up" reliability="75">
 				<dataResource>http://jjj.mib.ac.uk/index.html</dataResource>
 				<dataEntityExample>curien</dataEntityExample>
 				<dataEntry>http://jjj.mib.ac.uk/models/$id</dataEntry>
@@ -5792,7 +5819,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18832364</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100173" state="down" reliability="77">
+			<resource id="MIR:00100173" state="down" reliability="70">
 				<dataResource>http://pid.nci.nih.gov/</dataResource>
 				<dataEntityExample>pi3kcipathway</dataEntityExample>
 				<dataEntry>http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&amp;jpg=on&amp;pathway_id=$id</dataEntry>
@@ -5823,7 +5850,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12584128</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100174" state="up" reliability="97">
+			<resource id="MIR:00100174" state="up" reliability="96">
 				<dataResource>http://doqcs.ncbs.res.in/</dataResource>
 				<dataEntityExample>57</dataEntityExample>
 				<dataEntry>http://doqcs.ncbs.res.in/template.php?&amp;y=accessiondetails&amp;an=$id</dataEntry>
@@ -5859,7 +5886,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:12584128</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100175" state="up" reliability="97">
+			<resource id="MIR:00100175" state="up" reliability="96">
 				<dataResource>http://doqcs.ncbs.res.in/</dataResource>
 				<dataEntityExample>131</dataEntityExample>
 				<dataEntry>http://doqcs.ncbs.res.in/template.php?&amp;y=pathwaydetails&amp;pn=$id</dataEntry>
@@ -5905,7 +5932,7 @@
 				<dataInstitution>European Bioinformatics Institute, Hinxton, Cambridge</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100243" state="up" reliability="96">
+			<resource id="MIR:00100243" state="down" reliability="96">
 				<dataResource>http://bioportal.bioontology.org/ontologies/UO</dataResource>
 				<dataEntityExample>UO:0000080</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/UO/$id</dataEntry>
@@ -5943,7 +5970,7 @@
 				<dataInstitution>National Library of Medicine and ClinicalTrials.gov, Maryland</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100692" state="up" reliability="95">
+			<resource id="MIR:00100692" state="down" reliability="85">
 				<dataResource>http://clinicaltrials.bio2rdf.org/fct</dataResource>
 				<dataEntityExample>NCT00222573</dataEntityExample>
 				<dataEntry>http://clinicaltrials.bio2rdf.org/describe/?url=http://bio2rdf.org/clinicaltrials:$id</dataEntry>
@@ -6011,7 +6038,7 @@
 			<documentation type="URL">http://ncit.nci.nih.gov/ncitbrowser/pages/help.jsf</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100181" state="down" reliability="64">
+			<resource id="MIR:00100181" state="down" reliability="58">
 				<dataResource>http://ncit.nci.nih.gov/</dataResource>
 				<dataEntityExample>C80519</dataEntityExample>
 				<dataEntry>http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&amp;code=$id</dataEntry>
@@ -6048,7 +6075,7 @@
 			<documentation type="URL">http://www.biocatalogue.org/wiki/</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100182" state="up" reliability="93">
+			<resource id="MIR:00100182" state="up" reliability="94">
 				<dataResource>http://www.biocatalogue.org/</dataResource>
 				<dataEntityExample>614</dataEntityExample>
 				<dataEntry>https://www.biocatalogue.org/services/$id</dataEntry>
@@ -6062,14 +6089,14 @@
 		</tags>
 	</datatype>
 
-	<datatype id="MIR:00000141" pattern="^PR\:\d+$">
+	<datatype id="MIR:00000141" pattern="^PR\:P?\d+$">
 		<name>Protein Ontology</name>
 		<definition>The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies.</definition>
 		<uris>
 			<uri type="URN">urn:miriam:pr</uri>
 			<uri type="URL">http://identifiers.org/pr/</uri>
+			<uri type="URL" deprecated="true">http://identifiers.org/obo.pr/</uri>
 			<uri type="URN" deprecated="true">urn:miriam:obo.pr</uri>
-			<uri type="URL" deprecated="true">http://identifiers.org/obo.pr/</uri>
 		</uris>
 		<namespace>pr</namespace>
 		<documentations>
@@ -6077,7 +6104,7 @@
 			<documentation type="URL">https://pir5.georgetown.edu/wiki/PRO</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100184" state="up" reliability="99">
+			<resource id="MIR:00100184" state="down" reliability="95">
 				<dataResource>http://pir.georgetown.edu/pro/pro.shtml</dataResource>
 				<dataEntityExample>PR:000000024</dataEntityExample>
 				<dataEntry>http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$id</dataEntry>
@@ -6085,7 +6112,7 @@
 				<dataInstitution>Georgetown University Medical Center, Washington</dataInstitution>
 				<dataLocation>USA</dataLocation>
 			</resource>
-			<resource id="MIR:00100240" state="up" reliability="86">
+			<resource id="MIR:00100240" state="down" reliability="87">
 				<dataResource>http://bioportal.bioontology.org/ontologies/PR</dataResource>
 				<dataEntityExample>PR:000000024</dataEntityExample>
 				<dataEntry>http://purl.bioontology.org/ontology/PR/$id</dataEntry>
@@ -6338,7 +6365,7 @@
 				<dataInstitution>Europe PubMed Central partners</dataInstitution>
 				<dataLocation>UK</dataLocation>
 			</resource>
-			<resource id="MIR:00100747" state="up" reliability="97">
+			<resource id="MIR:00100747" state="down" reliability="94">
 				<dataResource>http://pubmedcentralcanada.ca/pmcc</dataResource>
 				<dataEntityExample>PMC3084216</dataEntityExample>
 				<dataEntry>http://pubmedcentralcanada.ca/pmcc/articles/$id</dataEntry>
@@ -6357,6 +6384,7 @@
 		</resources>
 		<tags>
 			<tag>bibliography</tag>
+			<tag>schema.org</tag>
 		</tags>
 		<annotation>
 			<format name="SBML">
@@ -6382,7 +6410,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19914931</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100193" state="down" reliability="87">
+			<resource id="MIR:00100193" state="down" reliability="78">
 				<dataResource>http://amoebadb.org/amoeba/</dataResource>
 				<dataEntityExample>EDI_244000</dataEntityExample>
 				<dataEntry>http://amoebadb.org/amoeba/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6408,7 +6436,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:16381902</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100194" state="down" reliability="86">
+			<resource id="MIR:00100194" state="down" reliability="78">
 				<dataResource>http://cryptodb.org/cryptodb/</dataResource>
 				<dataEntityExample>cgd7_230</dataEntityExample>
 				<dataEntry>http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6442,7 +6470,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18957442</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100195" state="down" reliability="86">
+			<resource id="MIR:00100195" state="down" reliability="78">
 				<dataResource>http://plasmodb.org/plasmo/</dataResource>
 				<dataEntityExample>PF11_0344</dataEntityExample>
 				<dataEntry>http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6476,7 +6504,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18824479</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100196" state="down" reliability="87">
+			<resource id="MIR:00100196" state="down" reliability="78">
 				<dataResource>http://giardiadb.org/giardiadb/</dataResource>
 				<dataEntityExample>GL50803_102438</dataEntityExample>
 				<dataEntry>http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6510,7 +6538,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19914931</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100197" state="down" reliability="86">
+			<resource id="MIR:00100197" state="down" reliability="78">
 				<dataResource>http://microsporidiadb.org/micro/</dataResource>
 				<dataEntityExample>ECU03_0820i</dataEntityExample>
 				<dataEntry>http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6544,7 +6572,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18003657</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100198" state="down" reliability="86">
+			<resource id="MIR:00100198" state="down" reliability="78">
 				<dataResource>http://toxodb.org/toxo/</dataResource>
 				<dataEntityExample>TGME49_053730</dataEntityExample>
 				<dataEntry>http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6578,7 +6606,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:18824479</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100199" state="down" reliability="86">
+			<resource id="MIR:00100199" state="down" reliability="78">
 				<dataResource>http://trichdb.org/trichdb/</dataResource>
 				<dataEntityExample>TVAG_386080</dataEntityExample>
 				<dataEntry>http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6615,7 +6643,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19843604</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100200" state="down" reliability="78">
+			<resource id="MIR:00100200" state="down" reliability="70">
 				<dataResource>http://tritrypdb.org/tritrypdb/</dataResource>
 				<dataEntityExample>Tb927.8.620</dataEntityExample>
 				<dataEntry>http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&amp;source_id=$id</dataEntry>
@@ -6652,7 +6680,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:15238527</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100201" state="up" reliability="93">
+			<resource id="MIR:00100201" state="up" reliability="94">
 				<dataResource>http://flypush.imgen.bcm.tmc.edu/pscreen/</dataResource>
 				<dataEntityExample>KG09531</dataEntityExample>
 				<dataEntry>http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$id</dataEntry>
@@ -6686,7 +6714,7 @@
 			<documentation type="PMID">urn:miriam:pubmed:19820115</documentation>
 		</documentations>
 		<resources>
-			<resource id="MIR:00100202" state="down" reliability="90">
+			<resource id="MIR:00100202" state="up" reliability="86">
 				<dataResource>http://beetlebase.org/</dataResource>
 				<dataEntityExample>TC010103</dataEntityExample>
 				<dataEntry>http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$id</dataEntry>
@@ -6772,7 +6800,...
 
[truncated message content]