Tracking issue for databases to import

[blakesweeney]

This issue is to track databases which could be good to import. We should review this issue each release to pick new databases. Additionally, whenever and interesting database is found it should be put into this list.

Once a database is chosen issues for that particular database for importing and how to best display the data should be created.

• [ ] MitoFun (https://github.com/RNAcentral/rnacentral-webcode/issues/496) Currently RNAcentral does not have a very good collection of fungal mito RNAs but we could obtain them from the following resource: http://mitofun.biol.uoa.gr/download.html http://mitofun.biol.uoa.gr/fasta/gGENE.fasta.zip
• [ ] RMDB: https://rmdb.stanford.edu/tools/ (https://github.com/RNAcentral/rnacentral-webcode/issues/138) In order to establish links with RMDB, we need to specify how a canonical sequence in RNAcentral ‘maps on’ to the sequence in RMDB. So far we haven't done any imports based on sequence mapping, but we will implement this approach for importing Rfam predictions. Once this is done, we can use the same procedure for RMDB.
• [ ] FunPEP (https://github.com/RNAcentral/rnacentral-webcode/issues/531) A new database of experimentally confirmed peptides found within lncRNAs: https://www.mdpi.com/2311-553X/6/4/41/htm
• [ ] lncDB (https://github.com/RNAcentral/rnacentral-webcode/issues/238) This database (http://www.bio-bigdata.com/Ubetis-LncDB/ I think) is a very high quality lncRNA database. We should treat data from it as being very reliable, according to John.
• [ ] OMIM (https://github.com/RNAcentral/rnacentral-webcode/issues/214) OMIM database links to Ensembl and HGNC which are already in RNAcentral so it should be possible to integrate with OMIM: http://www.omim.org/entry/614625?search=dancr
• [ ] LncRNAWiki (https://github.com/RNAcentral/rnacentral-webcode/issues/203) Example page: http://lncrna.big.ac.cn/index.php/ENST00000526269.2
• [ ] r-bind A database of molecules to bind to RNA, other than the ribosome. This could be very useful if we move toward more pharma work. Importing it might be adding annotations to specific sequences or maybe into Rfam families. https://rbind.chem.duke.edu/
• [ ] CircAtlas (PMID:32345360)
• [ ] circRNADb (PMID:27725737)
• [ ] CircFunBase (PMID:30715276)
• [ ] circBase (PMID:34195960)
• [ ] CIRCpedia (PMID:30172046)
• [ ] PlantCircNet (PMID:31725858)
• [ ] rnaapt3d (https://rnaapt3d.medals.jp/)
• [ ] Alliance of Genome Resource (https://www.alliancegenome.org/) - could be tricky since they pull from a bunch of MODs
• [ ] RISE (http://rise.life.tsinghua.edu.cn/index.html) - A database of RNA interactions
• [ ] Complex portal (https://www.ebi.ac.uk/complexportal/home) - Some ncRNAs are in complexes, so we should be able to cross link to them. They actually use our ids to annotate ncRNA so it should be simple. They also have some nice widgets could be useful to link to.
• [ ] GWAS Catalog (https://www.ebi.ac.uk/gwas/) - We could map their hits to our sequences both for display in the genome browser and the sequence feature viewer
• [ ] MitoFish - fish mito genomes: http://mitofish.aori.u-tokyo.ac.jp/
• [ ] FishExp - Expression data for fish: https://bioinfo.njau.edu.cn/fishExp/index.php
• [ ] Farm Gtex - expression data for farm animals: https://www.farmgtex.org/
• [ ] RNAInter - Database of RNA interactions: https://doi.org/10.1093/nar/gkab997, http://www.rnainter.org/
• [ ] MONARCH - Connecting phenotypes to genotypes across species: https://monarchinitiative.org/
• [ ] RNAChrom - database of RNA-Chromatin interactions: https://www.biorxiv.org/content/10.1101/2022.12.10.519346v1?ct=
• [ ] FANTOM (https://fantom.gsc.riken.jp/) Extremely rich dataset of funcitonal regions in genomes.
• [ ] Database of genomic variants (http://dgv.tcag.ca/dgv/app/home) Curated catalog of human structural variation - unclear if it has ncRNAs.
• [ ] SPENCER (http://spencer.renlab.org/#/home) Database of small peptides encoded by ncRNAs in cancer patients
• [ ] LncPep (http://www.shenglilabs.com/LncPep/#!/) the lncRNA coding peptides database
• [ ] CancerModels.org (https://www.cancermodels.org) a database of harmonized patient-derived cancer data