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diff --git a/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_17 b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_17 new file mode 100644 index 0000000..74708a3 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/gpt4o/intermediate_files/gpt4o_cs_gn_17 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2020 - Gene network a completely updated tool for systems genetics analyses.pdf", + "2020 - A platform for experimental precision medicine The extended BXD mouse family.pdf", + "2020 - GeneNetwork a toolbox for systems genetics.pdf", + "2017 - GeneNetwork a toolbox for systems genetics.pdf", + "2020 - Gene network a completely updated tool for systems genetics analyses.pdf", + "2011 - Using the PhenoGen Website for \u201cIn Silico\u201d Analysis of Morphine-Induced Analgesia Identifying Candidate Genes.pdf", + "2008 - Towards systems genetic analyses in barley Integration of phenotypic, expression and genotype data into GeneNetwork.pdf", + "2013 - Pathogenesis and reversal of liver fibrosis Effects of genes and environment.pdf", + "2012 - Genetic and Genomic Web Resources for Research on Alcohol Use and Abuse.pdf", + "2011 - Using the PhenoGen Website for \u201cIn Silico\u201d Analysis of Morphine-Induced Analgesia Identifying Candidate Genes.pdf" + ], + "extraction_id": [ + "858f630f-9443-5f13-ac40-8e16eadd9ba1", + "d1c32c32-42c8-5065-b7f2-bd2a0baeae62", + "2bdd2f18-e4d0-53e9-b0fa-a7ed8d710961", + "6cbea84e-4d8d-5ce0-8e58-45ee75f6f908", + "779b4029-6cc7-535e-a8b7-0ee31fa97162", + "0e3a5e40-06b0-58d4-b495-3093954ed17b", + "dc001755-2e77-5b41-8617-263b3ba35af8", + "71f1aefb-6e32-5add-804e-6fbaa39ca720", + "83ae495f-31a2-5977-a63a-57e704c394e2", + "0e3a5e40-06b0-58d4-b495-3093954ed17b" + ], + "document_id": [ + "128224f1-3545-52c3-93cb-77c3cf4ec70a", + "dd4994b9-9546-59c0-bc71-60e2617b6bcd", + "d11a87ca-4989-59af-95e3-ab90af7d9212", + "682c3a51-0aa5-54a3-a6e7-a09b81c0e8b6", + "128224f1-3545-52c3-93cb-77c3cf4ec70a", + "eb266fa1-8dec-5c56-a3d5-b508bd6bd448", + "8513abbe-65ed-5f35-9f86-ba93cfc5a194", + "73724c99-98df-53b2-a378-29c8b4faa171", + "08b12d72-9776-5acb-b1ef-7ee402781897", + "eb266fa1-8dec-5c56-a3d5-b508bd6bd448" + ], + "id": [ + "chatcmpl-AIGmdOlKLAeARCOPtbkwth6fOr9HL", + "c63cfaee-749e-547b-9c0a-086266f10670", + "bd2eb0ef-24a1-55ff-8597-c21dff0ecf0a", + "e030ce79-6970-5300-a1d8-1623d07c2157", + "1762dc59-0e50-5b7e-bdc2-b754e0e57797", + "f574ef17-062c-5bc8-be3e-81184e141970", + "fa07b1bf-94e6-515b-8400-cf3afa8b8741", + "251de62d-6e8e-50c7-9616-7fea05a250fb", + "f5c218f0-1280-55f8-912b-b32b833e93a3", + "db6bfa4e-9612-5f7e-8b7f-162f60b91c9d", + "0b2bd83d-680a-52d2-8116-50cce4f35cc3" + ], + "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", + "This paper analyzes existing, publicly available data. These data sets accession numbers are provided in the Key Resource Table , and throughout the manuscript. Genotype les can be found at http://www.genenetwork.org/webqtl/main.py?FormID= sharinginfo&GN_AccessionId=600 . GeneNetwork.org original code is publicly available at https://github.com/genenetwork/genenetwork2 and https://github.com/ genenetwork/genenetwork1 .", + "Fig. 2. GeneNetwork main search page and organization. Most analyses in GeneNetwork will follow the steps shown in panels A through D. In this workfl ow, a data set is selected ( A) and mined for traits of interest based on user search queries ( B). Traits are then selected from the search ( C) and placed in a collection for further inspection and quantitative analysis (D). The banner menu contains additional search options and helpful resources under the", + "Fig. 2. GeneNetwork main search page and organization. Most analyses in GeneNetwork will follow the steps shown in panels A through D. In this workfl ow, a data set is selected ( A) and mined for traits of interest based on user search queries ( B). Traits are then selected from the search ( C) and placed in a collection for further inspection and quantitative analysis (D). The banner menu contains additional search options and helpful resources under the", + "1. Data Once you have navigated to genenetwork.org, t here are two ways to search for data in GN. The first is to use the global search bar located at the top of the page (Figure 1 ). This is a new feature in GN that allows researchers to search for genes, mRNAs, or proteins across all of the datasets. This will give the user data for that search term across many different species, groups, and types of data. Because of this, the global search bar is a good area to start ones searches if", + "data are entered into GeneNetwork after they have been shepherded through a system like PhenoGen that has extensive capabilities for normalization and quality control. A comparison of the brain gene expression datasets and some of the tools for data analysis available on PhenoGen and GeneNetwork is shown in Table 3, and more detailed information on features provided by each site is outlined in the Supplementary DiscussionHoffman et al. Page 5 Addict Biol . Author manuscript; available in PMC 2012 July 1.", + "abundance data sets directly within GeneNetwork's ana- lytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (bar- ley) in a database that has been designed for an animal model species (mouse) with well established genome", + "GeneNetwork (www.genenetwork.org). The web -based software further allows extraction of sets of", + "need to read the help files, FAQs, or one of the references(Chesler et al., 2003; Grisham et al., 2010, www.lifescied.org/content/9/2/98.full.pdf). GeneNetwork is one ofan interlinked trio of sites built up by NIAAA (GeneWeaverand WebGestalt are the other two) to house extensivedata for human, monkey, rat, mouse, and fruit fly. Itincludes hundreds of data sets on responsesto alcohol,particularly in a family of mice called the BXDs. Dataare linked with powerful gene analysis and mappingtools. Think of it as", + "al., 2005). GeneNetwork is designed primarily as a web service for exploratory and statistical analysis of large published phenotype and genome datasets, and includes data from several species (see Supplementary Discussion). GeneNetwork includes extensive phenotype data extracted from the literature and submitted by users, which makes it practical to compare data on drug responses with gene expression patterns. Gene expression" + ], + "answer": "To access and use the data available on GeneNetwork.org, you can follow these steps: 1. **Navigating to the Website**: Start by visiting the GeneNetwork website at www.genenetwork.org [8]. 2. **Searching for Data**: There are two primary ways to search for data on GeneNetwork: - Use the global search bar located at the top of the page. This feature allows you to search for genes, mRNAs, or proteins across all datasets, providing data across various species, groups, and types of data [5]. - Alternatively, you can follow the main search workflow, which involves selecting a dataset, mining it for traits of interest based on user search queries, selecting traits from the search, and placing them in a collection for further inspection and quantitative analysis [3]. 3. **Analyzing Data**: Once you have selected the data, GeneNetwork provides an analytical environment where you can perform correlation analysis and linkage mapping. This environment helps identify and substantiate gene targets for further research [7]. 4. **Accessing Genotype Files**: If you need genotype files, they can be accessed directly via a specific URL: http://www.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600 [2]. 5. **Using Additional Resources**: The banner menu on the main search page contains additional search options and helpful resources to assist with your analyses [3]. By following these steps, you can effectively access and utilize the data available on GeneNetwork.org for your research needs.", + "question": "How can I access and use the data available on GeneNetwork.org?" +}
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