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Updated MIRIAM resources.
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@shoops
shoops committed Feb 3, 2025
1 parent 6d178bf commit e8eee27
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278 changes: 273 additions & 5 deletions copasi/MIRIAM/MIRIAMResources.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the -->
<!-- Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the -->
<!-- University of Virginia, University of Heidelberg, and University -->
<!-- of Connecticut School of Medicine. -->
<!-- All rights reserved. -->
Expand All @@ -19,10 +19,9 @@
<!-- and The University of Manchester. -->
<!-- All rights reserved. -->

<ParameterGroup name="Configuration">
<ParameterGroup name="MIRIAM Resources">
<Parameter name="LastUpdateDate" type="unsignedInteger" value="1678291289"/>
<Parameter name="Frequency" type="unsignedInteger" value="604800"/>
<Parameter name="LastUpdateDate" type="unsignedInteger" value="1738608731"/>
<Parameter name="Frequency" type="unsignedInteger" value="0"/>
<ParameterGroup name="Resources">
<ParameterGroup name="BIND">
<Parameter name="DisplayName" type="string" value="BIND"/>
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<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Genome assembly database - RefSeq accessions">
<Parameter name="DisplayName" type="string" value="Genome assembly database - RefSeq accessions"/>
<Parameter name="URI" type="string" value="urn:miriam:refseq.gcf"/>
<Parameter name="Pattern" type="string" value="^GCF_[0-9]{9}(\.[0-9]+)?$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Synapse Data Repository">
<Parameter name="DisplayName" type="string" value="Synapse Data Repository"/>
<Parameter name="URI" type="string" value="urn:miriam:synapse"/>
<Parameter name="Pattern" type="string" value="[0-9]*\.*[0-9]*"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Chemical Information Ontology">
<Parameter name="DisplayName" type="string" value="Chemical Information Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:cheminf"/>
<Parameter name="Pattern" type="string" value="^CHEMINF:\d+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="MediaDive mediums">
<Parameter name="DisplayName" type="string" value="MediaDive mediums"/>
<Parameter name="URI" type="string" value="urn:miriam:mediadive.medium"/>
<Parameter name="Pattern" type="string" value="^[A-Z]?[0-9]{1,5}[a-z]?$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Medical Action Ontology">
<Parameter name="DisplayName" type="string" value="Medical Action Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:maxo"/>
<Parameter name="Pattern" type="string" value="\d{7}"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Ontology for Parasite Lifecycle">
<Parameter name="DisplayName" type="string" value="Ontology for Parasite Lifecycle"/>
<Parameter name="URI" type="string" value="urn:miriam:opl"/>
<Parameter name="Pattern" type="string" value="^OPL:\d+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="BioDeep Database">
<Parameter name="DisplayName" type="string" value="BioDeep Database"/>
<Parameter name="URI" type="string" value="urn:miriam:biodeep"/>
<Parameter name="Pattern" type="string" value="^BioDeep_\d{11}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="DOME Registry">
<Parameter name="DisplayName" type="string" value="DOME Registry"/>
<Parameter name="URI" type="string" value="urn:miriam:dome"/>
<Parameter name="Pattern" type="string" value="^[a-z0-9]{10}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="NCBI Data Repository Service">
<Parameter name="DisplayName" type="string" value="NCBI Data Repository Service"/>
<Parameter name="URI" type="string" value="urn:miriam:ncbidrs"/>
<Parameter name="Pattern" type="string" value="^[0-9a-fA-F]{32}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Model Card Ontology">
<Parameter name="DisplayName" type="string" value="Model Card Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:mcro"/>
<Parameter name="Pattern" type="string" value="^MCRO:\d+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Integrated Chemical Environment - Chemical data">
<Parameter name="DisplayName" type="string" value="Integrated Chemical Environment - Chemical data"/>
<Parameter name="URI" type="string" value="urn:miriam:ice.chem"/>
<Parameter name="Pattern" type="string" value="\d{2,7}-\d{2}-\d|DTXSID\d{7,9}|[A-Z]{14}-[A-Z]{8}[SN][A-Z]-[A-Z]$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Mondo Disease Ontology">
<Parameter name="DisplayName" type="string" value="Mondo Disease Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:mondo"/>
<Parameter name="Pattern" type="string" value="^\d{7}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="tricdb">
<Parameter name="DisplayName" type="string" value="tricdb"/>
<Parameter name="URI" type="string" value="urn:miriam:tricdb"/>
<Parameter name="Pattern" type="string" value="^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Statistical Ontology">
<Parameter name="DisplayName" type="string" value="Statistical Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:stato"/>
<Parameter name="Pattern" type="string" value="^STATO:\d+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="LifeWatch Metadata Catalogue">
<Parameter name="DisplayName" type="string" value="LifeWatch Metadata Catalogue"/>
<Parameter name="URI" type="string" value="urn:miriam:lw"/>
<Parameter name="Pattern" type="string" value="^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Maggot">
<Parameter name="DisplayName" type="string" value="Maggot"/>
<Parameter name="URI" type="string" value="urn:miriam:maggot"/>
<Parameter name="Pattern" type="string" value="^[A-Za-z0-9]+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Human Chromosome Ontology">
<Parameter name="DisplayName" type="string" value="Human Chromosome Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:hco"/>
<Parameter name="Pattern" type="string" value="^.+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Ontology of Biological and Clinical Statistics">
<Parameter name="DisplayName" type="string" value=" Ontology of Biological and Clinical Statistics"/>
<Parameter name="URI" type="string" value="urn:miriam:obcs"/>
<Parameter name="Pattern" type="string" value="^OBCS:\d+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Metadata Management and distribution system for Multiple GNSS Networks">
<Parameter name="DisplayName" type="string" value="Metadata Management and distribution system for Multiple GNSS Networks"/>
<Parameter name="URI" type="string" value="urn:miriam:moid"/>
<Parameter name="Pattern" type="string" value="[a-zA-Z0-9]+\.[a-f0-9]{24}"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Biofactoid">
<Parameter name="DisplayName" type="string" value="Biofactoid"/>
<Parameter name="URI" type="string" value="urn:miriam:biofactoid"/>
<Parameter name="Pattern" type="string" value="^[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="ODAM Data explorer">
<Parameter name="DisplayName" type="string" value="ODAM Data explorer"/>
<Parameter name="URI" type="string" value="urn:miriam:odam.explorer"/>
<Parameter name="Pattern" type="string" value="^[A-Za-z][A-Za-z0-9]+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="CSTR">
<Parameter name="DisplayName" type="string" value="CSTR"/>
<Parameter name="URI" type="string" value="urn:miriam:cstr"/>
<Parameter name="Pattern" type="string" value="^\w{5}\.\d{2}\..*$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Austrian Library Network">
<Parameter name="DisplayName" type="string" value="Austrian Library Network"/>
<Parameter name="URI" type="string" value="urn:miriam:obv"/>
<Parameter name="Pattern" type="string" value="AC[0-9]{8}"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Gemeinsame Normdatei">
<Parameter name="DisplayName" type="string" value="Gemeinsame Normdatei"/>
<Parameter name="URI" type="string" value="urn:miriam:gnd"/>
<Parameter name="Pattern" type="string" value="[0-9X\-]+"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="OpenCitations Meta Identifier">
<Parameter name="DisplayName" type="string" value="OpenCitations Meta Identifier"/>
<Parameter name="URI" type="string" value="urn:miriam:omid"/>
<Parameter name="Pattern" type="string" value="^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="TogoVar">
<Parameter name="DisplayName" type="string" value="TogoVar"/>
<Parameter name="URI" type="string" value="urn:miriam:togovar"/>
<Parameter name="Pattern" type="string" value="^tgv[0-9]+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="VA Data Commons">
<Parameter name="DisplayName" type="string" value="VA Data Commons"/>
<Parameter name="URI" type="string" value="urn:miriam:dg.va03"/>
<Parameter name="Pattern" type="string" value="[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="Nanbyo Disease Ontology">
<Parameter name="DisplayName" type="string" value="Nanbyo Disease Ontology"/>
<Parameter name="URI" type="string" value="urn:miriam:nando"/>
<Parameter name="Pattern" type="string" value="^NANDO:[0-9]+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="1"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="AnVIL DRS">
<Parameter name="DisplayName" type="string" value="AnVIL DRS"/>
<Parameter name="URI" type="string" value="urn:miriam:drs.anv0"/>
<Parameter name="Pattern" type="string" value="^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
<ParameterGroup name="COG">
<Parameter name="DisplayName" type="string" value="COG"/>
<Parameter name="URI" type="string" value="urn:miriam:cog"/>
<Parameter name="Pattern" type="string" value="^COG[0-9]+$"/>
<Parameter name="Citation" type="bool" value="0"/>
<Parameter name="NamespaceEmbeddedInPattern" type="bool" value="0"/>
<ParameterGroup name="Deprecated">
</ParameterGroup>
</ParameterGroup>
</ParameterGroup>
</ParameterGroup>
</ParameterGroup>
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