## Things to add to GN AI
- `What is ensembl?`
It is good explanation, but you should put the related references that I didn't see.
Publications for ENSEMBL
Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John Tate, David Thybert, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D Finn, Kevin L Howe, Peter W Harrison, Andrew D Yates, and Paul Flicek
Ensembl 2023
Nucleic Acids Res. 2023, 51(D1):D933-D941
PMID: 36318249
doi:10.1093/nar/gkac958
Fiona Cunningham , James E. Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean , Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis , Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins , Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron , Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier , Toby Hunt, Thomas Juettemann , Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piliˇzota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-G ́omez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish , Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt , Garth R. IIsley, Jane E. Loveland , Fergal J. Martin , Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry , Magali Ruffier , John Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison , Kevin L. Howe , Andrew D. Yates , Daniel R. Zerbino and Paul Flicek
Ensembl 2022.
Nucleic Acids Res. 2022, vol. 50(1):D988-D995
PubMed PMID: 34791404.
doi:10.1093/nar/gkab1049
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G Izuogu, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj P Sakthivel, Ahamed I Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth R IIsley, Nick Langridge, Jane E Loveland, Fergal J Martin, Jonathan M Mudge, Joanella Morales, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Fiona Cunningham, Andrew D Yates, Daniel R Zerbino, Paul Flicek
Ensembl 2021.
Nucleic Acids Res. 2021, vol. 49(1):884–891
PubMed PMID: 33137190.
doi:10.1093/nar/gkaa942
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, José Carlos Marugán, Carla Cummins, Claire Davidson, Kamalkumar Dodiya, Reham Fatima, Astrid Gall, Carlos Garcia Giro´n, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, Thomas Maurel, Mark McDowall, Aoife McMahon, Shamika Mohanan, Benjamin Moore, Michael Nuhn, Denye N Oheh, Anne Parker, Andrew Parton, Mateus Patricio, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Mira Sycheva, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth IIsley, Myrto Kostadima, Nick Langridge, Jane E Loveland, Fergal J Martin, Joannella Morales, Jonathan M Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, Stephen J Trevanion, Fiona Cunningham, Kevin L Howe, Daniel R Zerbino, Paul Flicek
Ensembl 2020.
PubMed PMID: 31691826.
doi:10.1093/nar/gkz966
Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M. Ridwan Amode, Irina Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García Giro´n, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike Kay, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, José C Marugán, Thomas Maurel, Aoife C MacMahon, Benjamin Moore, Joannella Morales, Jonathan M Mudge, Michael Nuhn, Denye Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Andrew Yates, Daniel Zerbino, Paul Flicek
Ensembl 2019.
PubMed PMID: 30407521.
doi:10.1093/nar/gky1113
Sarah E Hunt, William McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Dan Sheppard, Andrew Parton, Irina M Armean, Stephen J Trevanion, Paul Flicek, Fiona Cunningham
Ensembl variation resources
Database Volume 2018
doi:10.1093/database/bay119
- Which database can I use for genetic, genomic, phenotype, and disease-related data generated from rat research?
The answer is RDG, it is okay. But please add the following right references.
- If I will ask what is RGD?
I had this issue:
Search_Query: what is RGD?
Status_Code: 500
Error/Reason: Request failed-'NoneType' object has no attribute 'status_code'
```
2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource.
Vedi M, Smith JR, Hayman GT, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Genetics 2023. iyad042. doi: 10.3390/genes13122304.
PMID: 36930729
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.
Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME.
Nucleic Acids Res. 2019 Nov 12. pii: gkz1041. doi: 10.1093/nar/gkz1041.
PMID:31713623
```
- What resources can I use to do pathway analyses?
You can use various resources for pathway analyses such as Ingenuity Pathway Analysis (IPA), Disease Association Protein-Protein Link Evaluator (DAPPLE), Pathway Studio, MetaCore, REACTOME, LitInspector, NetPath, Predictive Networks, GeneGo, Database for Annotation, Visualization and Integrated Discovery (DAVID), PATHWAYASSIST, E! Ensemble, Protonet, Pandora, Pubmatrix, KEGG, Reactome, g:Profiler, Gene Ontology, Biocarta, GenMAPP, WebGestalt, Gene Set Enrichment Analysis (GSEA), ClueGo, CluePedia, Cytoscape, RegulonDB, WIT.UM-BBD, EcoCyc, MetaCyc, Enzyme and metabolic pathways database, and Gene-Set Enrichment Analysis (GSEA).
The answer is quite okay but again you missed the tools references.
- You should remove IPA (IPA is a web-based bioinformatics application that allows researchers to upload data analysis results from high-throughput experiments such as microarray and next generation sequencing for functional analyze, integration, and further understanding. This includes both microarray and RNA-Seq gene expression, miRNA, SNP, metabolomics, and proteomics data. In general, lists of genes or chemicals can be analyzed using IPA. It also has a search capability for information on genes, proteins, chemicals, and drugs and allows interactive building of networks to represent biological systems), it is not used for our aim.
- You should remove Predictive Networks, because I didn't find any reference.
- You should remove E!Ensemble, is it ensembl? if yes it is not doing what we are asking.
- You should remove protonet, it is doing only analyses on protein
- You should remove PubMatrix: this a tool for multiplex literature mining, not in our aim
- You should remove GenMAPP because the project is no longer funded or actively supported
- WIT.UM-BBD: you should remove this, seems not related.
-
```
-DAPPLE: Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data
December 2016Methods in molecular biology (Clifton, N.J.) 1549:147-161 DOI: 10.1007/978-1-4939-6740-7_12
In book: Proteome BioinformaticsChapter: Bioinformatics Methods to Deduce Biological Interpretation from Proteomics DataPublisher: Springer New YorkEditors: Shivakumar Keerthikumar, Suresh Mathivanan
- Pathway studio: https://rc.umn.edu/msi/ipa-alternatives
- Metacore: https://www.metabolon.com/bioinformatics/pathway-analysis/
- Reactome: Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D’Eustachio P. The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research. 2024. doi: 10.1093/nar/gkad1025.
- LitInspector: Frisch M, Klocke B, Haltmeier M, Frech K. LitInspector: literature and signal transduction pathway mining in PubMed abstracts. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W135-40. doi: 10.1093/nar/gkp303. Epub 2009 May 5. PMID: 19417065; PMCID: PMC2703902.
- Netpath: https://www.solarwinds.com/network-performance-monitor/use-cases/netpath
- GeneGo: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927934/
- DAVID: B.T. Sherman, M. Hao, J. Qiu, X. Jiao, M.W. Baseler, H.C. Lane, T. Imamichi and W. Chang. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Research. 23 March 2022. doi:10.1093/nar/gkac194.
- Pathwayassist: Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio--the analysis and navigation of molecular networks. Bioinformatics. 2003 Nov 1;19(16):2155-7. doi: 10.1093/bioinformatics/btg290. PMID: 14594725.
- Pandora : Kelvin Xi Zhang, B. F. Francis Ouellette, Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence, Bioinformatics, Volume 26, Issue 4, February 2010, Pages 529–535, https://doi.org/10.1093/bioinformatics/btp701
- KEGG: Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000 Jan 1;28(1):27-30. doi: 10.1093/nar/28.1.27. PMID: 10592173; PMCID: PMC102409.
- g:Profiler: Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson: g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update) Nucleic Acids Research, May 2023; doi:10.1093/nar/gkad347.
- Gene Ontology: The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. DOI: 10.1093/genetics/iyad031
- BioCarta: BioCarta, Darryl NishimuraAuthors Info & Affiliations, Biotech Software & Internet Report:The Computer Software Journal for Scient https://doi.org/10.1089/152791601750294344
- Cytoscape:
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504
- GSEA software Subramanian, Tamayo, et al. (2005, PNAS) and Mootha, Lindgren, et al. (2003, Nature Genetics).
- ClueGO and CluePedia: Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-3
- RegulonDB: Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo JS, Alquicira-Hernández K, Martínez-Flores I, Pannier L, Castro-Mondragón JA, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Pérez-Rueda E, Alquicira-Hernández S, Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, Del Moral-Chávez V, Rinaldi F, Collado-Vides J. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 2016;44(D1):D133-43
- EcoCyc and MetaCyc:
Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform. 2016;17(5):877-90.
-Enzyme and metabolic pathways database - Likely referring to KEGG (Kyoto Encyclopedia of Genes and Genomes):
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
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