{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2023/09/09/making-bridgedb-derby-files-with-groovy.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/pn744-knt64", "url": "https://chem-bla-ics.linkedchemistry.info/2023/09/09/making-bridgedb-derby-files-with-groovy.html", "title": "Making BridgeDb Derby files with Groovy", "content_html": "

I just want to drop this here. There are various ways to make BridgeDb identifier mapping files. Some of the tools\npredate my joining the BiGCaT research group and the BridgeDb project, but this Groovy page is basically what we\nhave been using to create the metabolite identifier mapping databases:

\n\n
@Grab(group='org.bridgedb', module='org.bridgedb.bio', version='3.0.23')\n@Grab(group='org.bridgedb', module='org.bridgedb.rdb.construct', version='3.0.23')\n\nimport java.text.SimpleDateFormat;\nimport java.util.Date;\n\nimport org.bridgedb.IDMapperException;\nimport org.bridgedb.DataSource;\nimport org.bridgedb.Xref;\nimport org.bridgedb.bio.DataSourceTxt;\nimport org.bridgedb.rdb.construct.DBConnector;\nimport org.bridgedb.rdb.construct.DataDerby;\nimport org.bridgedb.rdb.construct.GdbConstruct;\nimport org.bridgedb.rdb.construct.GdbConstructImpl4;\n\nDataSourceTxt.init()\n\nGdbConstruct database = GdbConstructImpl4.createInstance(\n  \"test\", new DataDerby(), DBConnector.PROP_RECREATE\n);\ndatabase.createGdbTables();\ndatabase.preInsert();\n\ninchikeyDS = DataSource.getExistingBySystemCode(\"Ik\")\nlmDS = DataSource.getExistingBySystemCode(\"Lm\")\nswisslipidsDS = DataSource.getExistingBySystemCode(\"Sl\")\n\nString dateStr = new SimpleDateFormat(\"yyyyMMdd\").format(new Date());\ndatabase.setInfo(\"BUILDDATE\", dateStr);\ndatabase.setInfo(\"DATASOURCENAME\", \"LIPIDMAPS_SWISSLIPIDS\");\ndatabase.setInfo(\"DATASOURCEVERSION\", \"LIPID_TEST\");\ndatabase.setInfo(\"DATATYPE\", \"Metabolite\");\ndatabase.setInfo(\"SERIES\", \"standard_metabolite\");\n\nref1 = new Xref(\"YECLLIMZHNYFCK-RRNJGNTNSA-J\", inchikeyDS, true);\nref2 = new Xref(\"LMFA07050035\", lmDS, false);\ndatabase.addGene(ref1)\ndatabase.addGene(ref2)\ndatabase.addLink(ref1, ref1)\ndatabase.addLink(ref1, ref2)\n\nref3 = new Xref(\"SLM:000000493\", swisslipidsDS, true);\ndatabase.addGene(ref3)\ndatabase.addLink(ref1, ref3)\n\ndatabase.commit();\ndatabase.finalize();\n
\n\n

For the people who have worked with BridgeDb Java in the past, note the new SQL schema 4, as used by the\nGdbConstructImpl4. This schema allows indicating of an identifiers is outdated/retired/etc. This is\nactually the case for the LMFA07050035 identifiers, and hence the false parameter in the new Xref()\ncall.

", "summary": "I just want to drop this here. There are various ways to make BridgeDb identifier mapping files. Some of the tools predate my joining the BiGCaT research group and the BridgeDb project, but this Groovy page is basically what we have been using to create the metabolite identifier mapping databases:", "date_published": "2023-09-09T00:00:00+00:00", "date_modified": "2023-09-09T00:00:00+00:00", "tags": ["groovy","bridgedb"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }