From e8eee2786dfdfbf6fd21263900452e395b7befce Mon Sep 17 00:00:00 2001 From: Stefan Hoops Date: Mon, 3 Feb 2025 13:55:20 -0500 Subject: [PATCH] Updated MIRIAM resources. --- copasi/MIRIAM/MIRIAMResources.xml | 278 +++++++++++++++++++++++++++++- copasi/MIRIAM/miriam.xml | 253 ++++++++++++++++++++++++++- 2 files changed, 523 insertions(+), 8 deletions(-) diff --git a/copasi/MIRIAM/MIRIAMResources.xml b/copasi/MIRIAM/MIRIAMResources.xml index 7f336a7b8d..f5ba5e0234 100644 --- a/copasi/MIRIAM/MIRIAMResources.xml +++ b/copasi/MIRIAM/MIRIAMResources.xml @@ -1,5 +1,5 @@ - + @@ -19,10 +19,9 @@ - - - + + @@ -7691,6 +7690,275 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - diff --git a/copasi/MIRIAM/miriam.xml b/copasi/MIRIAM/miriam.xml index 05c844862c..1c71e5a4de 100644 --- a/copasi/MIRIAM/miriam.xml +++ b/copasi/MIRIAM/miriam.xml @@ -1,5 +1,5 @@ - + @@ -25180,7 +25180,7 @@ operated by California Digital Library, Crossref, and Datacite. Stress Knowledge Map - Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. + Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. skm urn:miriam:skm @@ -25252,7 +25252,7 @@ operated by California Digital Library, Crossref, and Datacite. UTRdb - A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. + A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. utrdb urn:miriam:utrdb @@ -25266,6 +25266,253 @@ operated by California Digital Library, Crossref, and Datacite. urn:miriam:biokc + + Genome assembly database - RefSeq accessions + The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage. + refseq.gcf + + urn:miriam:refseq.gcf + + + + Synapse Data Repository + Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate. + synapse + + urn:miriam:synapse + + + + Chemical Information Ontology + The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals. + cheminf + + urn:miriam:cheminf + + + + MediaDive mediums + MediaDive is a manually curated collection of cultivation media and growth conditions. This namespace specifically references mediums. + mediadive.medium + + urn:miriam:mediadive.medium + + + + Medical Action Ontology + An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. + maxo + + urn:miriam:maxo + + + + Ontology for Parasite Lifecycle + The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. + opl + + urn:miriam:opl + + + + BioDeep Database + The BioDeep database is a comprehensive database of metabolite information in living organisms: by aggregating metabolite information from multiple public databases and large-scale natural language text mining work, we have built a large scale knowledge network for biological knowledge interpretation. By using the BioDeep database, it is possible to query such large scale metabolic knowledge network. + biodeep + + urn:miriam:biodeep + + + + DOME Registry + A database of annotations for published papers describing machine learning methods in biology + dome + + urn:miriam:dome + + + + NCBI Data Repository Service + This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. + ncbidrs + + urn:miriam:ncbidrs + + + + Model Card Ontology + An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). + mcro + + urn:miriam:mcro + + + + Integrated Chemical Environment - Chemical data + The Integrated Chemical Environment (ICE) provides high-quality curated data and appropriate tools to support development and evaluation of new, revised, and alternative methods. ICE provides free online access to curated in vivo and in vitro test data, in silico toxicity predictions and chemical property data, reference chemical lists, and computational tools for chemical characterization and predicting toxicity. +ICE supports the following: (i) Data integration: brings together available data, including data on formulations; (ii) Results exploration: enables dynamic, graphical exploration with publication-quality graphics; (iii) Data analysis: allows characterization of data using online workflows, and (iv) FAIR data access: data are findable, accessible, interoperable, and reusable. + ice.chem + + urn:miriam:ice.chem + + + + Mondo Disease Ontology + The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. + mondo + + urn:miriam:mondo + + + + tricdb + Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine. + tricdb + + urn:miriam:tricdb + + + + Statistical Ontology + STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. + stato + + urn:miriam:stato + + + + LifeWatch Metadata Catalogue + The LifeWatch Metadata Catalogues plays a crucial role in managing metadata for digital objects, including Datasets, Services, Workflows and Virtual Research Environments. This catalogue serves as the central repository, ensuring that resources are accessible and reusable by stakeholders. + lw + + urn:miriam:lw + + + + Maggot + Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond. + maggot + + urn:miriam:maggot + + + + Human Chromosome Ontology + The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes. + hco + + urn:miriam:hco + + + + Ontology of Biological and Clinical Statistics + OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI) + obcs + + urn:miriam:obcs + + + + Metadata Management and distribution system for Multiple GNSS Networks + M3G stands for “Metadata Management and distribution system for Multiple GNSS Networks”. M3G allows to upload, validate, and distribute GNSS station metadata such as IGS-style site logs, information about local networks, DOIs, nominal data provision, data licenses attached to the daily RINEX data, etc... + moid + + urn:miriam:moid + + + + Biofactoid + Biofactoid is a resource of biological pathways, assembled from author-curated results in papers. + + biofactoid + + urn:miriam:biofactoid + + + + ODAM Data explorer + ODAM (Open Data for Access and Mining) is an Experimental data table management software (EDTMS) to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines. + +ODAM allows datasets to be explored and then extracted in whole or in part as needed. + +For more information/explanation, see ODAM User's Guide : https://inrae.github.io/ODAM/ + odam.explorer + + urn:miriam:odam.explorer + + + + CSTR + CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. + cstr + + urn:miriam:cstr + + + + Austrian Library Network + The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections. + obv + + urn:miriam:obv + + + + Gemeinsame Normdatei + The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners. + gnd + + urn:miriam:gnd + + + + OpenCitations Meta Identifier + Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted. + omid + + urn:miriam:omid + + + + TogoVar + TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. + togovar + + urn:miriam:togovar + + + + VA Data Commons + The VA Data Commons supports the research and analysis of US military Veteran medical and genomic data and aims to accelerate scientific discovery and development of therapies, diagnostic tests, and other technologies for improving the lives of Veterans and beyond. + + dg.va03 + + urn:miriam:dg.va03 + + + + Nanbyo Disease Ontology + Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan. + nando + + urn:miriam:nando + + + + AnVIL DRS + This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. + drs.anv0 + + urn:miriam:drs.anv0 + + + + COG + Database of Clusters of Orthologous Genes (COGs). This database defines all orthologs of protein sequences coded by known genomes. The species name, protein name, and phylogenetic tree of orthologous clusters can be viewed through this site. Each cluster is comprised of individual proteins and its paralogs, matched to evolutionarily conserved molecular domains. + cog + + urn:miriam:cog + + annotation