BioHackathon-projects-2019:该存储库供2019年11月在巴黎举办的BioHackathon的参与者共享

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  • 2022-04-02 03:41
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欧洲生物黑客马拉松2019 : 该存储库供2019年11月在巴黎举办的BioHackathon的参与者使用,以共享想法,创建问题,管理项目,发布材料,创建代码等。 请求访问此仓库 可以通过gitter通道请求对此存储库的访问 ,包括您的GitHub用户名或以下GitHub中的。 专案 (按项目编号排序) :罕见疾病的疾病和途径图 :副本编号变更信标 :使用Galaxy和Carpentries培训材料可扩展地交付生命科学领域的FAIR培训 :走向无缝的Galaxy和InterMine集成:增强的区域分析 :文本挖掘和语义Web技术 :生物化学领域学术出版物的知识图 项目14 :全功能:实时监控计算工作流 项目15 :实施Orphanet和Orphadata的生物模式 项目22 :RO形状轮廓,BrAPI和生物化学形状验证 项目25 :根据ELIXIR准则设计软件管理计划
BioHackathon-projects-2019-master.zip
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# Implementation of Bioschema for Orphanet and Orphadata **Project Number:** 15 ## Orphanet DEV environment links (not public, need VPN) Nb: JSON-LD is displayed in the page to show it (=> will be put into script tags obviously) Nb: real implementation will need a new constructor within the framework engine (to optimize integration) Nb: it works (=> possible to search different drugs, tradename, genes, diseases...) Nb: we provide permalinks to jsonplayground to visualize implementation Tradename example (http://dev.orpha.net/hanauer/consor4.01/www/cgi-bin/Drugs_Search.php?lng=EN&data_id=2583&Substance=VINCERINONE&Typ=Med&title=VINCERINONE&data_type=Product) JSON PLAYGROUND (https://tinyurl.com/s7fdw5z) Drugs example (http://dev.orpha.net/hanauer/consor4.01/www/cgi-bin/Drugs_Search.php?lng=EN&data_id=2082&Tradename=Alpha-tocotrienol-quinone&Typ=Sub&title=Alpha-tocotrienol%20quinone&data_type=Product) JSON PLAYGROUND (https://tinyurl.com/s8f4znm) Gene example (http://dev.orpha.net/hanauer/consor4.01/www/cgi-bin/Disease_Genes.php?lng=EN&data_id=20738&Disease_Disease_Genes_diseaseGroup=brca1&Disease_Disease_Genes_diseaseType=Gen&MISSING%20CONTENT=BRCA1-associated-protein-1---BAP1&search=Disease_Genes_Simple&title=BRCA1%20associated%20protein%201%20-%20BAP1) JSON PLAYGROUND (https://tinyurl.com/tgppjv5) Disease example (http://dev.orpha.net/hanauer/consor4.01/www/cgi-bin/Disease_Search.php?lng=EN&data_id=91&Disease_Disease_Search_diseaseGroup=rett&Disease_Disease_Search_diseaseType=Pat&Disease(s)/group%20of%20diseases=Rett-syndrome&title=Rett%20syndrome&search=Disease_Search_Simple) JSON PLAYGROUND (https://tinyurl.com/qu7xf8x) Disease HPO annotations example (http://dev.orpha.net/hanauer/consor4.01/www/cgi-bin/Disease_HPOTerms.php?lng=EN&data_id=8&Disease_Disease_HPOTerms_diseaseGroup=canavan&Disease_Disease_HPOTerms_diseaseType=Pat&Disease(s)/group%20of%20diseases=Canavan-disease&title=Canavan%20disease&search=Disease_HPOTerms_Simple) JSON PLAYGROUND (https://tinyurl.com/yx2bqnqt) ## Docker image of Orphadata's FAIRdatapoint done and running ! Giving a machine readable access to Orphadata's datasets Need a bit more look&feel customisation (http://purl.org/orphadata/fairpoint) ## Research area alignment - Elxir Core Data Resources Rare disease Elixir Communities Federated Data ## Team **Submitter:** Marc Hanauer ### Proponent(s) - Marc Hanauer ### Lead(s) - Marc Hanauer David Lagorce ## Background information --- Orphanet is a website dedicated to rare diseases, providing several kind of information such nomenclature, classifications, textual information, disorders/genes relations and also dedicated resources in the field (Experts centres, Diagnostic tests, clinical trials, orphandrugs, registries and biobanks, supports groups etc.) for more than 40 countries. The site has a huge audience, around 2 million unique visitors/month and 8 languages. ![Orphanet](https://raw.githubusercontent.com/elixir-europe/BioHackathon/master/interoperability/Development%20of%20a%20catalog%20of%20federated%20SPARQL%20queries%20in%20the%20field%20of%20Rare%20Diseases/images/Orphanet.png) The database content is linked to the Orphanet nomenclature ![Orphanet_Map](https://github.com/elixir-europe/BioHackathon/blob/master/interoperability/Development%20of%20a%20catalog%20of%20federated%20SPARQL%20queries%20in%20the%20field%20of%20Rare%20Diseases/images/ORPHANET-map.png) and we provide several dataset, also accessible on our platform Orphadata https://www.orphadata.org ![Orphadata](https://github.com/elixir-europe/BioHackathon/raw/master/interoperability/Development%20of%20a%20catalog%20of%20federated%20SPARQL%20queries%20in%20the%20field%20of%20Rare%20Diseases/images/Screenshot_Orphadata.png) Orphanet produce also the Orphanet Rare Diseases Ontology and clinical description of diseases using HPO ontology. Each disease concept has a unique, stable, identifier (Orphacode) which could be used to identify diseases in health information system. The orphacode has been integrated in several countries. ![Codification](https://github.com/elixir-europe/BioHackathon/raw/master/interoperability/Development%20of%20a%20catalog%20of%20federated%20SPARQL%20queries%20in%20the%20field%20of%20Rare%20Diseases/images/map-codificationOrpha2018.jpg) ### Nominated participant(s) - Rajaram Kaliyaperumal (FAIR expert) Celine Rousselot (Orphanet PHP dev lead) David Lagorce (Orphanet/Orphadata project manager & Dev) Marc Hanauer (Orphanet CTO) & Thomas Rosnet (IFB) (Please note: no travel fundings for Rousselot, Lagorce and Hanauer, only accommodation) ## Expected outcomes - Improve interoperability of our core data resources FAIRdatapoint avalaible ## Expected audience - FAIR expert PHP dev. (Orphanet's website) data model (RDF/Ontology) **Number of expected hacking days**: 4 ## Existing Repo Orphanet website https://github.com/Orphanet/orphanet_website_biohack2019 Orphadata website https://github.com/davidlagorce/orphadata_website_biohack2019
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