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diff --git a/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_18 b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_18 new file mode 100644 index 0000000..6db16f1 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_18 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2020 - Gene network a completely updated tool for systems genetics analyses.pdf", + "2018 - Genetic Networks Activated by Blast Injury to the Eye.pdf", + "2010 - Systems genetics analyses predict a transcription role for P2P-R Molecular confirmation that P2P-R is a transcriptional co-repressor.pdf", + "2012 - Using Genome-Wide Expression Profiling to Define Gene Networks Relevant to the Study of Complex Traits From RNA Integrity to Network Topology.pdf", + "2013 - Pathogenesis and reversal of liver fibrosis Effects of genes and environment.pdf", + "2011 - Peroxisomal L-bifunctional enzyme (Ehhadh) is essential for the production of medium-chain dicarboxylic acids.pdf", + "2021 -Highlights from the Era of Open Source Web-Based Tools.pdf", + "2020 -Highlights from the Era of Open Source Web-Based Tools.pdf", + "2020 - Gene network a completely updated tool for systems genetics analyses.pdf", + "2015 - Gene network of a phosphoglycerate mutase in muscle wasting in mice.pdf" + ], + "extraction_id": [ + "858f630f-9443-5f13-ac40-8e16eadd9ba1", + "0c76461f-34ff-5604-aa4c-12eb9d2877aa", + "ec624ebb-489a-5437-a721-f01cf981d0a7", + "3e0c2a06-e6de-5888-a360-a2c483d9f744", + "71f1aefb-6e32-5add-804e-6fbaa39ca720", + "a8b40857-7ae8-512a-9817-bea1ae3345ba", + "62c12bdc-ae2b-5cc0-88f5-a3c1a264326b", + "28892088-5a95-56eb-822d-b12da3a612d0", + "858f630f-9443-5f13-ac40-8e16eadd9ba1", + "b71c7c43-8bd9-5d7e-b337-a8c0396f96b7" + ], + "document_id": [ + "128224f1-3545-52c3-93cb-77c3cf4ec70a", + "57e3820f-7a5d-51f1-a0c6-ecfbdf546005", + "e4d1e2e9-f267-5814-8c7b-dc11d7eec9bf", + "1eb6f5b7-a3bc-5455-91f0-6f2eb37be861", + "73724c99-98df-53b2-a378-29c8b4faa171", + "ac61753e-bcb2-55c3-804b-e821e3d1a4ad", + "0a6f3d2e-70c3-5db7-bfc0-93ad04806104", + "f2f0dc2f-eaf5-57f6-9ffa-816d3fab6640", + "128224f1-3545-52c3-93cb-77c3cf4ec70a", + "912c42f2-1802-5fe9-b9dd-871c5290dd18" + ], + "id": [ + "chatcmpl-AIGmkanSOkp2jhcX3KUkfSSqCSJEs", + "c63cfaee-749e-547b-9c0a-086266f10670", + "105b8e0a-a88c-59a6-9d39-7d894d059b73", + "a9508122-3b14-5365-979c-ba580bdcb78f", + "312eae52-ede7-5c13-8974-fce0126426cf", + "f5c218f0-1280-55f8-912b-b32b833e93a3", + "8b8a24da-a175-5cb8-91bd-8966fca5d344", + "aaf19f3a-353a-595b-b7de-da9f01a7b0f1", + "7b626f27-5aed-5464-a20d-463954ff057d", + "f3f859bb-d066-5552-b07e-eefcb489d8f5", + "a0c173a5-8685-50df-8110-8d7ec02cdbf3" + ], + "contexts": [ + "GeneNetwork have reinvigorated it, including the addition of data from 10 species, multi -omics analysis, updated code, and new tools. The new GeneNetwork is now an exciting resource for predictive medicine and systems genetics, which is constantly being maintained and improved. Here, we give a brief overview of the process for carrying out some of the most common functions on GeneNetwork, as a gateway to deeper analyses , demonstrating how a small", + "18 GeneNetwork Time Machine : Full versions from 2009 to 2016 (mm9); UTHSC Genome Browser Classic and Newest ; UTHSC Galaxy Servic e; UTHSC Bayesian Network Web Server ; GeneNetwork Classic on Amazon Cloud ; GeneNetwork Classic Code on GitHub ; GeneNetwork 2.0 Development Code on GitHub ; and GeneNetwork 2.0 Development. Technologies or techniques: None Inventions, patent applications, and/or licenses: None Other products: None", + "GeneNetwork http://www.genenetwork.org is anexample of a bioinformatics tool that can be used to explore systems genetics data. The importance of defining biological networks and predicting molecular interactions has been emphasized by several reports [1,2]. Such studies emphasize that when knowledge about DNA variation within popula- tions is interfaced with data on gene expression, protein interactions and DNA-protein binding, biological networks can be constructed that are predictive of the", + "addition to this, GeneNetwork can be used to study correlations between traits and to perform data mining in genomic regions containing candidates for quantitative trait genes (Hoffman et al., 2011). All datasets in GeneNetwork are linked to a materials and methods information page that summarizes experimental details relating to the dataset. Databases within GeneNetwork include the transcriptome database, the BXD published", + "GeneNetwork (www.genenetwork.org). The web -based software further allows extraction of sets of", + "subnetworks GeneNetwork (www.genenetwork.org) is a depository of data- sets and tools for use in complex systems biology approaches in order to generate or predict higher order gene function ( 23, 24 ).", + "distributed neuroscience data sharing with ever expanding prospects for future breakthroughs. GeneNetwork.org : genetic analysis for all neuroscientists Originally named webqtl, GeneNetwork.org is the oldest contin- uously operating website in biomedical research ( Williams, 1994). This massive database contains ;40 million datasets. GeneNetwork.org also offers a powerful statistical platform for online network analyses and mapping, enabling numerous mo-", + "distributed neuroscience data sharing with ever expanding prospects for future breakthroughs. GeneNetwork.org : genetic analysis for all neuroscientists Originally named webqtl, GeneNetwork.org is the oldest contin- uously operating website in biomedical research ( Williams, 1994). This massive database contains ;40 million datasets. GeneNetwork.org also offers a powerful statistical platform for online network analyses and mapping, enabling numerous mo-", + "1 GeneNetwork: a continuously updated tool for systems genetics analyses Pamela M. Watson1, David G. Ashbrook1 1Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA Abstract GeneNetwork and its earlier iteration , WebQTL, have now been an important database and toolkit for quantitative trait genetics research for two decades. Recent improvements to", + "resources, gene expression pro les, and gene network constructions, methods for the analysis of gene function have been revolutionised in the past few years. One great resource for the analysis of gene networks is the databaseGeneNetwork, which consists of a set of linked resources for systems genetics (Andreux et al., 2012). It has been designed for multiple scale integration of networks of genes,transcripts in multiple tissues. GeneNetwork is an interac-" + ], + "answer": "The provided context does not explicitly mention any specific recent discoveries made using GeneNetwork.org. However, it highlights the platform's capabilities and improvements, such as the addition of data from 10 species, multi-omics analysis, updated code, and new tools, which make it a valuable resource for predictive medicine and systems genetics [1]. Additionally, GeneNetwork.org is described as a powerful statistical platform for online network analyses and mapping, which could enable numerous breakthroughs in neuroscience and other fields [7]. While these improvements and capabilities suggest potential for discoveries, specific recent discoveries are not detailed in the context provided.", + "question": "What are some recent discoveries made using GeneNetwork.org?" +}
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