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@@ -1,2 +1,7 @@ gnqa/paper2_eval/data/testresp2.json gnqa/paper2_eval/src/__pycache__/document_operations.cpython-310.pyc +gnqa/paper2_eval/configparser +gnqa/paper2_eval/sys +gnqa/paper2_eval/pd +gnqa/paper2_eval/os +gnqa/paper2_eval/json diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_1 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_1 new file mode 100644 index 0000000..81d5073 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_1 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2017 - Regular exercise participation improves genomic stability in diabetic patients an exploratory study to analyse telomere length and DNA damage.pdf", + "2020 - Clinical Genetics and Genomics of Aging.pdf", + "2008 - Telomeres and Aging.pdf", + "2006 - Sex-specific telomere length profiles.pdf", + "2018 - Sex Differences in Aging Genomic Instability.pdf", + "2002 - Mitochondrial dysfunction leads to telomere attrition.pdf", + "2006 - Sex-specific telomere length profiles.pdf", + "2017 - The Aging Cardiovascular System.pdf", + "2020 - Clinical Genetics and Genomics of Aging.pdf", + "2018 - Repetitive Fragile Sites Centromere Satellite DNA.pdf" + ], + "extraction_id": [ + "0e53122e-a308-55f7-8ee8-a0857ac9c52f", + "efd18101-9cf2-56b5-8f86-c2aba6caa0bc", + "13990eb4-bef2-58ce-bf3e-0e3bc294caab", + "6d3bfe47-f26e-50dc-8d77-19f3797e53a0", + "396708f1-aa0a-571e-a8d3-7cb8404e9502", + "b92ede07-74a7-524a-8d2c-54b2559e8425", + "eb8d8e40-a484-57cb-8125-3fd5eb3f6389", + "6949970f-7bc7-5585-a57a-96de1b5ba6ec", + "d4afa45a-5efa-577b-822e-7a82c2f6508d", + "3b0cb0ab-421d-54d7-9816-c6a2e6f1ac68" + ], + "document_id": [ + "dcaf7b09-2d54-5cbf-b061-e3c4e6c6c518", + "62b635c3-040e-512a-b016-6ef295308a1e", + "61d9c326-d36e-55c1-a891-335dc943e70f", + "09c78a17-4a1f-52c1-be4d-994fd9fd71d0", + "8cfb5529-7f0c-58fc-b6e4-b3ee800fb72f", + "d8bc729b-7513-58b7-b12e-0db1fb6d3b7d", + "09c78a17-4a1f-52c1-be4d-994fd9fd71d0", + "d3ff8471-986b-5fa0-b9c4-96eaaa8fce7c", + "62b635c3-040e-512a-b016-6ef295308a1e", + "262df0d6-ad68-544a-88ed-b4568f305858" + ], + "id": [ + "chatcmpl-ABLwBBugt6fTuTWqXb74qvoPVubbX", + "bb069c10-45f1-5a83-95e3-4b7655874ba7", + "28e98b7e-f273-5bdd-9979-185133f311af", + "5f940245-af1d-5eee-84dc-942017c523d0", + "607cbd31-d430-5517-8212-208b25af32bf", + "53508a9e-d064-58a3-a4f9-0785470a1462", + "7fad29bd-12bf-53d0-af89-aadd38b974ff", + "64ef9964-1831-5a7a-8a69-5e8d0c332d37", + "1b453e12-a0c4-59db-a978-bbebd689e7dc", + "65fb74aa-f3c3-5c80-919f-329169db982f", + "f181e6da-58b6-5f26-87a2-355e25388673" + ], + "contexts": [ + "repetitive nucleotide sequences at the end of each eukaryotic chromosome, which protects them from attrition and damage. Although the relationship between leukocyte telomere length (LTL) and diabetes is still questioned 8, different studies have shown that T2D individuals have shorter leukocyte telomeres than non-T2D individuals9, 10 that may be associated with disease progression11. Indeed, the decreased antioxidant capacity described in patients", + "Telomeres are arrays of linked nucleotide hexamer repeats that are found at the ends of chromosomes in a vast clade of organisms [14]. While the sequence of these telomeric repeats can vary between organisms, their biological function is highly conserved, which is to limit damage inflicted on genes during the replica- tion of chromosomes. Telomere length is progressively shortened with each round of genomic replication, unless it is restored through the action of a ribonucleo-", + "telomere length,a phenomenon attributed to higher levels of oxidativestress at the cellular level (70). More recent studies havelinked telomere length in smooth muscle cells with senes-cence and disease severity in patients with atherosclero-sis (141, 150). Leukocyte telomere length was also short ina cohort of similar patients and associated with a higherrisk of developing occult cardiovascular disease (71).More data are needed to understand and validate the useof leukocyte telomere length as a biomarker", + "age telomere length through accumulation of several short telo- meres (Londono-Vallejo et al., 2001; Martens et al., 2000) is responsible for senescence or whether a speci c chromosome arm limits the replication potential of human cells (Hemann et al., 2001). Individual chromosome arms were shown to have large variations in their length (Lansdorp et al., 1996; Benn, 1997; Londono-Vallejo et al., 2001), and chromosome 17p seemed to be equipped with especially short telomeres in hu-", + "Telomeres are specialized structures that protect the ends of linear chromosomes. They shorten during aging due to the unidirectional activity of DNA polymerase, which leaves a section of DNA unrepli-cated on the lagging strand. Telomeres also are subject to shortening by genotoxic stress, such as oxidative damage (33). Among many eukaryotes, the enzyme telomerase maintains telomere length; but telomerase activity varies over the lifespan and between cell types, tissues, and species (34). In most human", + "TTAGGG sequence that cap the ends of chromosomes, protect-ing them from degradation and fusion. The length of telomererepeats is primarily maintained by active telomerase, which iscomposed of Telomerase RNA (TR) and a catalytic subunitTelomerase Reverse Transcriptase (TERT) (Blackburn, 2001).Extensive evidence has shown that telomere shortening anderosion lead to chromosome end-to-end fusions and genomicinstability (Blasco et al ., 1997; Hande et al ., 1999), causing", + "a pivotal role in maintenance of genomic integrity and func-tion (Moyzis et al., 1988; McElligott and Wellinger, 1997; van Steensel and de Lange, 1997). It is generally accepted that telomeres shorten during DNA replication both in vitro and in vivo. In individuals, short telomeres are considered to be a sign of advanced age. Cawthon and coworkers (2003) showed that telomere shortening in hu-", + "Each cell division shortens telomeric DNA until, at a critical length, the cells lose capping function at thechromosomal ends, activating DNA damage check-points, cell senescence, and eventually apoptosis.Telomere shortening has particular relevance in thesetting of CVD. Leukocyte telomere length (LTL) associates signi cantly with vascular cell senescence,", + "nization may directly affect telomere attrition, resulting in accelerated replicative senescence and progeroid phenotypes [180]. Telomeres are regions constituted by tandem repeats of non-coding DNA sequences 5-(TTAGGG)n-3 and a protein complex called shelterin, bound to them. This structure ensures the stability of the genome and protects the chromosomes from a wrong action of the DNA repair machinery [184] by allowing the formation of a chromatin loop called T-Loop [185].", + "telomeres, the repetitive sequence at the end of linear chromosomes, has garnered much attention for its relation to aging. Telomere repeats serve as an internal clock for cycling cells because each round of replication results in the loss of telomeric DNA in the absence of active telomerase (reviewed in [66]). Eventually, this loss over cellular generations culminates in telomere crisis and a permanent state of" + ], + "answer": "The length of telomeres is significant for several reasons: 1. **Protection of Chromosomes**: Telomeres are repetitive nucleotide sequences at the ends of eukaryotic chromosomes that protect them from attrition and damage during replication [1], [2], [6]. They prevent the loss of important genetic information and maintain genomic stability [9]. 2. **Aging and Cellular Senescence**: Telomere length is progressively shortened with each round of genomic replication unless restored by the enzyme telomerase [2], [5]. Short telomeres are considered a sign of advanced age and are associated with cellular senescence, where cells lose their ability to divide and function properly [4], [7], [8]. 3. **Disease Association**: Shorter telomeres have been linked to various diseases. For instance, individuals with Type 2 Diabetes (T2D) have been shown to have shorter leukocyte telomeres, which may be associated with disease progression [1]. Similarly, telomere length in smooth muscle cells has been linked to disease severity in atherosclerosis, and shorter leukocyte telomeres are associated with a higher risk of developing cardiovascular disease [3], [8]. 4. **Genomic Integrity**: Telomeres play a crucial role in maintaining genomic integrity and function. Shortening and erosion of telomeres can lead to chromosome end-to-end fusions and genomic instability, which can cause various cellular dysfunctions and diseases [6], [7]. 5. **Biomarker Potential**: Due to their association with aging and disease, telomere length is being studied as a potential biomarker for various health conditions, including cardiovascular diseases and diabetes [3]. In summary, the length of telomeres is crucial for protecting chromosomes, regulating cellular aging, and maintaining genomic stability. It also has significant implications for understanding and potentially diagnosing age-related diseases and conditions.", + "question": "What is the significance of the length of telomeres?" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_2 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_2 new file mode 100644 index 0000000..c4e6321 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_2 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf", + "2021 - Footprints in the Sand Deep Taxonomic Comparisons in Vertebrate Genomics to Unveil the Genetic Programs of Human Longevity.pdf", + "2021 - Genetic loci and metabolic states associated with murine epigenetic aging.pdf", + "2021 -Mozhui- Epigenetic aging.pdf", + "2016 - Unraveling the message insights into comparative genomics.pdf", + "2012 - Chromatin Remodeling, DNA Damage Repair and Aging.pdf", + "2021 - Gene-by-environment modulation of lifespan and weight gain in the murine BXD family.pdf", + "2006 - THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM_PROG.pdf", + "2012 - Genome-Scale Studies of Aging Challenges and Opportunities.pdf", + "2003 - Lifelong voluntary exercise in the mouse prevents.pdf" + ], + "extraction_id": [ + "5cc56e3b-53ab-5299-814d-014e2ed31d2f", + "11ca91fa-a13f-5cc5-90c8-53d1ebe76836", + "a9ebf1d8-5ef8-5c52-962e-110873476823", + "e662d80d-b529-5749-856c-ed734c6e3eaa", + "c6f50e80-1bc5-5b0a-b57b-4c2bfe524d96", + "d9a12bd9-c65e-547a-89aa-4e0231558ddc", + "30ba3324-6e19-58c2-9e32-508f827af3e5", + "c04cac81-a0b0-5d0a-b21e-2f94494bb302", + "9669b6fe-e9d7-55e8-a91a-c015df633daa", + "6a2cdf66-f3c9-5be9-b6b0-f203be169103" + ], + "document_id": [ + "ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b", + "0dc45abe-ab02-5b07-9916-7093b53323c0", + "b82bd9e1-2373-577b-a942-164565eaca6b", + "d23daa43-4176-54e6-b3c3-b889843e92f1", + "0deba7bb-c27a-5d9e-b1b2-e48a5574882c", + "594e5dbe-b92a-5b0c-9f65-2a10670f9517", + "4d082da4-fa48-5170-8147-c4fea47a5d4b", + "b84914bc-195d-5c48-8e89-0db719675c1f", + "b77aace0-fa36-5fd4-8e2a-c8932198acd1", + "24d4f270-f45b-5830-84f9-b1e5bcd3c070" + ], + "id": [ + "chatcmpl-ABLwRFLcOLGvXJuXhHs6NCge9tY7Z", + "09da6f9e-b996-5438-91be-41d9438cb930", + "14bf5e8a-4095-536f-b98b-00c8cdae3a31", + "f8fdd2ee-710c-5d2c-8a70-bf48f4927653", + "e613d3df-adb0-56b0-abfd-8828020c23c3", + "02296a91-f1a4-5b35-a5d1-e1851797404b", + "90214d4d-4068-5490-9049-5604b5dcf3e2", + "56e03e38-0ae5-5b29-b929-662fa091e0ac", + "ebc5b444-a63f-5819-9d3a-ffbf96b3d367", + "80d01818-7573-5321-b33d-c7e291f3fe74", + "11af155f-85c6-5f8b-8943-5391ad678f7e" + ], + "contexts": [ + "11. Gelman R, Watson A, Bronson R et al (1988) Murine chromo- somal regions correlated with longevity. Genetics 118(4):693704 12. Jackson AU, Galecki AT, Burke DT et al (2002) Mouse loci associated with life span exhibit sex-specic and epistatic effects. J Gerontol A Biol Sci Med Sci 57(1):B9B15 13. Foreman JE, Lionikas A, Lang DH et al (2009) Genetic archi- tecture for hole-board behaviors across substantial time intervalsin young, middle-aged and old mice. Genes Brain Behav", + "Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PLoS Genet. 14:e1007272. doi: 10.1371/journal.pgen.100 7272 Schchter, F., Faure-Delanef, L., Gunot, F., Rouger, H., Froguel, P., Lesueur-Ginot, L., et al. (1994). Genetic associations with human longevity at the APOE and ACE loci. Nat. Genet. 6, 2932. doi: 10.1038/ng0194-29 Schinaman, J. M., Rana, A., Ja, W. W., Clark, R. I., and Walker, D. W. (2019).", + "of the mouse growth hormone receptor results in severely decreased body weights, insulin, and insulin- like growth factor I levels and increased life span. Endocrinology 144:37993810. DOI: https://doi.org/10.1210/en. 2003-0374, PMID: 12933651 de Haan G, Williams RW. 2005. A genetic and genomic approach to identify longevity genes in mice. Mechanisms of Ageing and Development 126:133138. DOI: https://doi.org/10.1016/j.mad.2004.09.012, PMID: 15610771", + "of the mouse growth hormone receptor results in severely decreased body weights, insulin, and insulin- like growth factor I levels and increased life span. Endocrinology 144:37993810. DOI: https://doi.org/10.1210/en. 2003-0374, PMID: 12933651 de Haan G, Williams RW. 2005. A genetic and genomic approach to identify longevity genes in mice. Mechanisms of Ageing and Development 126:133138. DOI: https://doi.org/10.1016/j.mad.2004.09.012, PMID: 15610771", + "Mulvey L, Sinclair A, Selman C (2014) Lifespan modulation in mice and the confounding effects of genetic background. J Genet Genomics 41:497503. doi: 10.1016/j.jgg.2014.06.002 OConnor TP, Lee A, Jarvis JUM, Buffenstein R (2002) Prolonged longevity in naked mole-rats: age-related changes in metabolism, body composition and gastrointestinal function. Comp Biochem Physiol A 133:835842. doi: 10.1016/S1095-6433(02)00198-8 Opazo JC, Palma RE, Melo F, Lessa EP (2005) Adaptive evolution of", + "/ mice by Lmna heterozy- gosity ameliorates progeroid phenotypes and extends lifespan [143, 174, 175].", + "References 1. Hook Met al.Genetic cartography of longevity in humans and mice: Current landscape and horizons. Biochim. Biophys. Acta1864, 27182732 (2018). 2. Kuningas Met al.Genes encoding longevity: from model organisms to humans. Aging Cell7, 270 280 (2008). [PubMed: 18208581] 3. de Magalhes JP, Wuttke D, Wood SH, Plank M & V ora C Genome-environment interactions that modulate aging: Powerful targets for drug discovery. Pharmacol. Rev. 64, 88101 (2012). [PubMed: 22090473]", + "\"Murine chromosomal regions correlated with longevity.\" Genetics 118: 693-704.", + "expression of alpha-1,2-mannosidase I extends lifespan in Drosophila melanogaster and Caenorhabditis elegans . Aging Cell, 2009 , 8(4), 370-9. [73] Wang, H.D.; Kazemi-Esfarjani, P.; Benzer, S. Multiple-stress analysis for isolation of Drosophila longevity genes . Proc Natl Acad Sci U S A , 2004 , 101(34), 12610-5. [74] Lin, Y.J.; Seroude, L.; Benzer, S. Extended life-span and stress resistance in the Drosophila mutant methuselah . Science , 1998 , 282(5390), 943-6.", + "sion analysis of mouse liver genes: effect of age and of thelongevity mutant Prop1df. J Gerontol A Biol Sci Med Sci 56: B72B80, 2001. 12.Fabrizio P, Pozza F, Pletcher SD, Gendron CM, and Longo VD. Regulation of longevity and stress resistance by Sch9 in Yeast. Science 292: 288 290, 2001. 13.Haase D, Lehmann MH, Korner MM, Korfer R, Sigusch HH, and Figulla HR. Identi cation and validation of selective" + ], + "answer": "The mouse genes associated with longevity include: 1. **Mouse loci associated with life span**: These loci exhibit sex-specific and epistatic effects [1]. 2. **Mouse growth hormone receptor**: Alterations in this gene result in increased lifespan [3], [4]. 3. **Lmna heterozygosity**: This genetic modification ameliorates progeroid phenotypes and extends lifespan [6]. These references provide evidence of specific genes and loci in mice that have been linked to increased longevity.", + "question": "Which mouse genes have been associated with longevity?" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_3 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_3 new file mode 100644 index 0000000..1f78fa9 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_3 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2009 - The Human Ageing Genomic Resources online.pdf", + "2011 - How pleiotropic genetics of the musculoskeletal system.pdf", + "2021 - Genome-wide association studies identify.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2020 - Clinical Genetics and Genomics of Aging.pdf", + "2001 - A genome-wide scan for linkage to human.pdf", + "2007 - Temporal and spatial transcriptional profiles.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2020 - Role of Helicobacter pylori infection in the manifestation of old age-related diseases.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf" + ], + "extraction_id": [ + "7ada6b55-99c2-5e20-bf96-d153f927256c", + "b5b3c74a-90de-5b1e-9580-8031b10be7ec", + "cd7730b6-22dc-5256-9310-79fc348b3226", + "d59d7882-333d-5576-86ab-3cfa6354b946", + "4ea8424f-1cd8-569c-a1df-3f0f54206e70", + "17246c43-2e44-579b-867d-3dc7150ceedd", + "2e42619b-d0b2-5d33-aab8-6f04002ee807", + "d59d7882-333d-5576-86ab-3cfa6354b946", + "e6916baa-9f9d-57aa-b44d-95fb614610a8", + "a01ca925-4ccf-5863-a162-7bd4c754fe89" + ], + "document_id": [ + "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529", + "ed31486c-a651-5894-bd96-21fbd78f2646", + "60c2e869-1fee-53ea-b332-26d9c2abc747", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "62b635c3-040e-512a-b016-6ef295308a1e", + "1431984a-82d9-51d4-a23c-5f76a02ab554", + "38f27ec7-08bf-5397-b2b8-bde95e0dc3f8", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e99c68d2-4f35-5591-8072-cfdb31966e68", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec" + ], + "id": [ + "chatcmpl-ABLwW9HA9VG184zgOmenEBU2eMIMc", + "3117c019-7311-53ae-8ab1-927ca822c709", + "0ad664d2-6756-5123-b192-8a56cf6887a5", + "9fa00091-9661-57bd-91c7-f0bf436805a7", + "786d2756-4c4d-5ac0-8d3d-63f914d51664", + "a0672677-71ad-5603-8427-a0648eec407f", + "e0cce1c5-8709-5218-99b6-48a6ba242931", + "bf2cd208-273f-5848-b243-df8b95ea7833", + "413f8f54-b5cc-5089-9f5c-d9e3b8bcf594", + "50581d4f-396c-5d12-aec6-5f42e2ab88ef", + "3c369292-4b9c-5156-a80f-4b3301026f30" + ], + "contexts": [ + "It is undisputed that genetic factors influence aging. In a remarkable", + "perform a study of the genetic sources of biological aging. However, to be successful, the genetic study of acomplex condition requires a heritable phenotype to be developed and validated. Genome-wide association studies offer an unbiased approach to identify newcandidate genes for human diseases. It is hypothesized that convergent results from multiple aging-related traits will point out the genes responsible for the general agingof the organism. This perspective focuses on the", + "population dynamics on the genetic architecture of human longevity. Aging (Albany NY). 2018;10(8):1947 63. 68. Bellenguez C, Kucukali F, Jansen I, Andrade V, Morenau-Grau S, Amin N, et al. Large meta-analysis of genome-wide association studies expands knowledge of the genetic etiology of Alzheimer disease and highlights potential translational opportunities. medRxiv. 2020. 69. Kojima T, Shimazui T, Hinotsu S, Joraku A, Oikawa T, Kawai K, et al. Decreased expression of CXXC4 promotes a", + "In addition to aging- and CR-related genes, another source of candidate genes and pathways for drug designare human longevity-associated genes (Barzilai andShuldiner, 2001; Browner et al., 2004; Kenyon, 2010).Dozens of genes have now been associated with humanlongevity (de Magalha es et al., 2009a), although only ahandful of genes have been shown to have consistenteffects across populations. Many longevity-associated genes are related to spe-", + "Clinical Genetics and Genomics of Aging", + "effect fundamental mechanisms of aging (14, 16). The drawbacksof such studies include the improbability of picking the right geneto study the myriad of known and unknown genes affecting theprocess of interest (17). The linkage study described heremarkedly improves the efficiency of such association studies bydefining a region likely to contain polymorphism(s) with signif-icant influence on life span. Additional association studies with these families and repli-", + "The multifactorial and temporal features of aging can beanalyzed efficiently by genome-wide transcriptional profiling,which has been conducted in various model organisms and hu-mans (Melov and Hubbard 2004). Aging is associated with alter-ations in transcript levels of many genes, including those in-volved in evolutionarily conserved mitochondrial and protea-somal functions (McCarroll et al. 2004), some of which havebeen shown to be directly involved in regulating lifespan in C.", + "overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,", + "Mol Genet Genomic Med. 2020;00:e1157. | 1 of 11 https://doi.org/10.1002/mgg3.1157 wileyonlinelibrary.com/journal/mgg3 1 | INTRODUCTION Aging is one of the inevitably dominant risk associated with many diseases. Several biological factors contribute to this etiology which", + "al., 2009; Stanfel et al., 2009). Many of these genesmodulate the response to environmental signals, such asfood availability, and act in signaling pathways that ifunderstood can be targeted (Fig. 1). The genetic regula-tion of aging is therefore an emerging field with multipleapplications in the human nutrition, cosmetic, and phar-maceutical industries. AGING GENES AS TARGETS FOR DRUG DISCOVERY 91" + ], + "answer": "Genetic factors associated with aging include: 1. **Genome-wide association studies (GWAS)**: These studies offer an unbiased approach to identify new candidate genes for human diseases, including those related to aging. Convergent results from multiple aging-related traits can point out the genes responsible for the general aging of the organism [2]. 2. **Longevity-associated genes**: Dozens of genes have been associated with human longevity, although only a handful have shown consistent effects across populations. These genes are often related to specific biological pathways and processes [4]. 3. **Genes involved in mitochondrial and proteasomal functions**: Aging is associated with alterations in the transcript levels of many genes, including those involved in evolutionarily conserved mitochondrial and proteasomal functions. Some of these genes have been shown to be directly involved in regulating lifespan [7]. 4. **Genes with protective functions**: Certain genes that are overexpressed with age seem to have protective functions, helping organisms manage aging. These genes could be targets for manipulation to potentially influence the aging process [8]. These genetic factors highlight the complex interplay of various genes and pathways in the aging process.", + "question": "what genetic factor are associated with aging" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 new file mode 100644 index 0000000..09d1513 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2009 - The Human Ageing Genomic Resources online.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2011 - Clinical aspects and molecular diagnostics of skin aging.pdf", + "2015 - Transcriptomic profiles of aging in purified.pdf", + "2004 - A Transcriptional Profile of Aging.pdf", + "2020 - A multidimensional systems biology.pdf", + "2011 - Metabolism, Genomics, and DNA Repair in the Mouse Aging Liver.pdf", + "2010 - MicroRNA, mRNA, and protein expression link.pdf", + "2012 - GeneFriends An online co-expression analysis.pdf" + ], + "extraction_id": [ + "d59d7882-333d-5576-86ab-3cfa6354b946", + "52c67b46-63f2-54ae-a78e-e9d54a55f6e4", + "d59d7882-333d-5576-86ab-3cfa6354b946", + "674e1da7-73d5-5101-b5a5-4981e483123c", + "e5fd1ff0-8df5-577f-9f2d-31b0941d5ce5", + "8b47c304-ee91-5c52-8324-79fd0bd32b27", + "9d1656aa-32d2-5094-8232-4817655b1cbd", + "a6a6b5ba-3a72-55c5-91bb-abe747624348", + "fc9974c9-2e48-5a08-9112-0109df9ce096", + "1839dfa6-7080-5de4-96cb-3493ca2056d3" + ], + "document_id": [ + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e32f8f2c-d3ad-5dae-a393-9bd87c370ebe", + "50f357a3-e0f2-5e32-a6b2-771fb4b1e1c6", + "4ab656a7-9656-526b-94e1-422875409b44", + "d040bfe3-e409-5b5c-b8f8-f3dd4fc060e3", + "a94fd15d-373e-51c5-ad74-a17e4260d32a", + "c3ae47b0-42dd-5ab0-8fec-a41831d1bbfa", + "be20af52-c782-5098-893a-9a92000bf5a0" + ], + "id": [ + "chatcmpl-ABLwhCwS1z9hZBn1zWSbHm5JcD7CF", + "b719fbc0-94e4-5df0-abb7-0d13fc36214c", + "8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb", + "413f8f54-b5cc-5089-9f5c-d9e3b8bcf594", + "896169ed-4b9b-5ebc-9c9d-1cd2e6f3437c", + "6b4fb407-fd3f-52a3-9cfd-07dc5c891dd5", + "17ce11f7-55df-59bd-a801-a6f38ae9a9ef", + "61baeaa5-d65a-54b5-bfee-9bab8bbf1985", + "3414ff44-7d60-5492-9956-353ab9a94a43", + "b2d47567-09dc-5c77-be72-9448aa954e6b", + "1c3f7772-e1fa-5063-bda7-04b2f7e7b0e3" + ], + "contexts": [ + "lar signatures of mammalian aging. Some of the genes", + "www.ncbi.nlm.nih.gov/homologene) of genes strongly asso-ciated with aging in model organisms. Also included are genesin which mutations result in segmental progeroid syndromes,such as the Werners syndrome gene, as well as genes criticalin pathways previously related to aging, such as the insulin/insulin-like signalling pathway (de Magalhes et al ., 2005a). The", + "overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,", + "expression profile of aging in human muscle. Physiol Genomics 2003;14:149-59. 142. Rodwell GE, Sonu R, Zahn JM. A transcriptional profile of aging inthe human kidney. PLoS Biol 2004;e427:2. 143. Hasty P, Campisi J, Hoeijmakers J, van Steeg H, Vijg J. Aging and genome maintenance: lessons from the mouse? Science 2003;299:1355-9. 144. Kyng KJ, May A, Klvraa S, Bohr VA. Gene expression profiling in Werner syndrome closely resembles that of normal aging. Proc Natl Acad Sci U S A 2003;100:12259-64.", + "neurodegenerative diseases. Nature. 2006;443:787 95. 50. de Magalhes JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009;25:875 81. 51. Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, et al. AGEMAP: a gene expression database for aging in mice. PLoS Genet. 2007;3:e201. 52. Liu LF, Shen WJ, Ueno M, Patel S, Kraemer FB. Characterization of age- related gene expression profiling in bone marrow and epididymal", + "Ly DH, Lockhart DJ, Lerner RA, Schultz PG (2000) Mitotic misregulation and human aging. Science 287: 24862492. McCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, et al. (2004) Comparing genomic expression patterns across species identies shared transcriptional prole in aging. Nat Genet 36: 197204. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, et al. (2003) Genes that act downstream of DAF-16 to inuence the lifespan of Caenorhabditis elegans Nature 424: 277283.", + "genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build", + "exhibits important alterations in global gene expressionproles with age. In mice, aging is accompanied by changesin expression of genes associated with increased inamma-tion, cellular stress, brosis, altered capacity for apoptosis,xenobiotic metabolism, normal cell-cycle control, and DNAreplication [ 5]. Lifelong calorie restriction reversed the", + "stance, genes associated with energy production, which decrease their expression during aging across various tissues and species (Zahn et al. 2006, 2007; de Magalha es et al. 2009), start decreasing at this transition point in our data (group 5; Fig. 2A). Hence, 25 yr of age in humans may mark the beginning of systemic change associated with certain senescence processes. Conservation of expression changes with age We observe that both developmental and aging expression pro-", + "p <10 -6; Table 1 shows the top 25 genes. Many of these genes have been associated with age-related diseases.Several other genes that have been shown to play a role in aging such as lysosomal-associated membrane protein-2 Lamp2 [19] (p = 5.68 -30), Fas [20] (p = 2.70-31) and growth hormone receptor Ghr [21] (p = 1.34-19) also showed a significant co-expression. Anxa2, Anxa3 and Anxa4 also show a low p-value (p < 10-25) as well as several S100 calcium binding proteins which have been" + ], + "answer": "Genes typically associated with early aging include those involved in segmental progeroid syndromes, such as the Werner syndrome gene [2]. Additionally, genes critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway, are also associated with early aging [2].", + "question": "which genes are typically associated with early aging?" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_5 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_5 new file mode 100644 index 0000000..c0b3b7f --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_5 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2001 - A genome-wide scan for linkage to human.pdf", + "2023 - A transcriptome-based single-cell biological age model.pdf", + "2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf", + "2007 - Longevity Genomics Across Species.pdf", + "2020 - Clinical Genetics and Genomics of Aging.pdf", + "2017 - Systems genetic analysis in GeneNetwork.org.pdf", + "2021 - Gene-by-environment modulation of lifespan and weight gain in the murine BXD family.pdf", + "2016 - Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging.pdf", + "2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf", + "2009 - Meta-analysis of age-related gene expression profiles identifies.pdf" + ], + "extraction_id": [ + "17246c43-2e44-579b-867d-3dc7150ceedd", + "0fd46f00-d3e1-54f4-9395-6c3e8294ed51", + "5cc56e3b-53ab-5299-814d-014e2ed31d2f", + "522e2616-daa1-5bf3-8673-a717dfb9b13f", + "5c3840bd-45a5-5928-84ab-a1f2d8536691", + "59121146-02b9-5479-96e2-9fb45cffc81b", + "396683f9-b2e3-5942-bec8-f96fa798c341", + "382122b9-6922-5d85-9e8c-acfa86aff085", + "df0b4be9-3393-5642-a722-ccafffb60df8", + "4d95f551-34bd-5e7a-8702-eb59de73a480" + ], + "document_id": [ + "1431984a-82d9-51d4-a23c-5f76a02ab554", + "9be234b7-f37d-5cd5-8895-bfe676441b2f", + "ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b", + "1ab0b63f-d97c-5f5c-98ee-0bde785fa630", + "62b635c3-040e-512a-b016-6ef295308a1e", + "41be0f9f-a5af-5586-b6cd-16e56fd89cdc", + "4d082da4-fa48-5170-8147-c4fea47a5d4b", + "8cde78ac-cb0e-5983-86ee-91074b2fe1e3", + "ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b", + "5c2cf97f-a57a-5284-85a3-b8d9c5943113" + ], + "id": [ + "chatcmpl-ABLwlxjoJ15UXMdKPBfDnYfvZNLDD", + "e0cce1c5-8709-5218-99b6-48a6ba242931", + "9f9fef49-0bda-5948-93bd-0f8f43bbefdf", + "09da6f9e-b996-5438-91be-41d9438cb930", + "ab0845d4-b4db-53db-927e-b96a52cf7667", + "c2299f0f-9e0b-5279-90e5-37c6bd664976", + "3004d1fd-c5ce-5587-bfab-471e7141952c", + "9082d164-59f8-58a0-ace7-8b3aa9d884e2", + "7abf14d2-cdfe-5c37-8217-6b63bd8fb255", + "380ca35e-b42b-59b4-aef7-aaf2ba3bb59d", + "eea576fd-d766-5ae7-9e63-045869a3f8f7" + ], + "contexts": [ + "effect fundamental mechanisms of aging (14, 16). The drawbacksof such studies include the improbability of picking the right geneto study the myriad of known and unknown genes affecting theprocess of interest (17). The linkage study described heremarkedly improves the efficiency of such association studies bydefining a region likely to contain polymorphism(s) with signif-icant influence on life span. Additional association studies with these families and repli-", + "Map contains 1119 and 1459 curated human and mouse aginggenes, respectively, covering almost all scales of aging, rangingfrom molecular damage to genetic predisposition. Cross-speciescomparison revealed a modest overlap between known humanand mouse aging genes, suggesting both conservation of core sen- escence pathways and fundamental differences in aging between mice and humans (Fig. 2E). Aging-associated genes can alternatively be identified in a", + "11. Gelman R, Watson A, Bronson R et al (1988) Murine chromo- somal regions correlated with longevity. Genetics 118(4):693704 12. Jackson AU, Galecki AT, Burke DT et al (2002) Mouse loci associated with life span exhibit sex-specic and epistatic effects. J Gerontol A Biol Sci Med Sci 57(1):B9B15 13. Foreman JE, Lionikas A, Lang DH et al (2009) Genetic archi- tecture for hole-board behaviors across substantial time intervalsin young, middle-aged and old mice. Genes Brain Behav", + "Along with longevity, a select group of potential aging-related biomarkers will be assayed for each of these mouse models. In addition, it should be possible to assay several of these mouse lines for resistance to specific age-associated diseases, such as diabetes and neurological disorders, by crossing them into the appropriate transgenic disease back- ground. CONCLUSION Our understanding of the basic mechanisms of aging have benefited greatly from the use of simple model systems", + "198 the study of age-related diseases for various reasons: (a) mice are closely related to humans, with nearly 99% of human orthologous in mice; (b) their relatively short lifespan and small size allow surveillance of the aging process within a pertinent time frame and make their housing less expensive; (c) the feasibility of performing genetic manipulations facilitates the engineering of transgenic strains (gain- and loss-of function mice) that model premature aging disorders. In this section, we", + "Hsu HC, Lu L, Yi N, Van Zant G, Williams RW, Mountz JD. Quantitative trait locus (QTL) mapping in aging systems. Methods in Molecular Biology (Clifton, NJ ). 2007; 371:321348. Hunter KW, Crawford NPS. The future of mouse QTL mapping to diagnose disease in mice in the age of whole-genome association studies. Annual Review of Genetics. 2008; 42:131141. Ito R, Robbins TW, Everitt BJ. Differential control over cocaine-seeking behavior by nucleus", + "multiscalar integration of traits. Cell150, 12871299 (2012). [PubMed: 22939713] 33. De Haan G & Van Zant G Genetic analysis of hemopoietic cell cycling in mice suggests its involvement in organismal life span. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 13, 707713 (1999). 34. Gelman R, Watson A, Bronson R & Yunis E Murine chromosomal regions correlated with longevity. Genetics 118, 693704 (1988). [PubMed: 3163317] 35. Houtkooper RHet al.The metabolic footprint of aging in mice. Sci. Rep1, (2011).", + "mice to identify genetic factors involved in the regulation of cognitive aging that may have gone undetected in either complex human studies or murine studies utilizing only a single genetic background. Aging is a leading risk factor for age-associated de- mentias such as AD, and our work and others suggest that geneticfactors and mechanisms underlying biological processes during midlife play a key role in determining an individual s susceptibility", + "span and have yielded insights into potential biological pathways and processes related to aging. Despite these successes, several problems are inherent in human longevity studies including potentially high degrees ofenvironmental heterogeneity, genetic diversity, and lack of birth matched controls, among others [ 8]. Inbred mouse strains represent a powerful alternative for identifying genes underlying complex trait genes such as longevity [ 9]. Initial mapping approaches include quanti-", + "Recently, the Atlas of Gene Expression in Mouse Aging Project (AGEMAP) reported gene expression proles with age for 8932genes in 16 mouse tissues (Zahn et al ., 2007). We chose not to" + ], + "answer": "To generate a linkage or association mapping study in mice to understand aging, you can follow these steps: 1. **Select Appropriate Mouse Strains**: Choose inbred mouse strains that are known to have variations in lifespan and aging-related traits. Inbred strains are powerful for identifying genes underlying complex traits such as longevity due to their genetic uniformity [9]. 2. **Identify Aging-Related Traits**: Determine the specific aging-related traits you want to study. This could include longevity, resistance to age-associated diseases, or other biomarkers of aging [4]. 3. **Cross Mouse Strains**: Perform crosses between different inbred strains to generate F1 and F2 generations. This helps in creating genetic diversity necessary for mapping studies [5]. 4. **Phenotyping**: Assay the F2 generation (or other relevant generations) for the aging-related traits of interest. This could involve measuring lifespan, resistance to diseases, or other biomarkers [4]. 5. **Genotyping**: Genotype the mice using molecular markers such as SNPs (Single Nucleotide Polymorphisms) to identify genetic variations across the genome [6]. 6. **Quantitative Trait Locus (QTL) Mapping**: Use QTL mapping techniques to identify chromosomal regions associated with the aging-related traits. This involves statistical analysis to correlate genetic markers with phenotypic traits [6]. 7. **Association Studies**: Conduct association studies to further refine the regions identified by QTL mapping. This involves looking for specific polymorphisms within the identified regions that are significantly associated with the traits [1]. 8. **Replication and Validation**: Validate the findings by replicating the study in different mouse populations or using additional genetic crosses. This helps to confirm the association between the identified genetic regions and aging traits [1]. By following these steps, you can generate a linkage or association mapping study in mice to understand the genetic factors influencing aging.", + "question": "How do I generate a linkage or association mapping study in mice to understand aging?" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_6 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_6 new file mode 100644 index 0000000..8e291e1 --- /dev/null +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_6 @@ -0,0 +1,65 @@ +{ + "titles": [ + "2010 - A Meta-analysis of Four Genome-Wide Association Studies.pdf", + "2014 - Whole-Genome Sequencing of the World?s Oldest People.pdf", + "2011 - Genome-wide association study identifies a single major locus contributing to survival into old age the APOE locus revisited.pdf", + "2017 - Four Genome-Wide Association Studies Identify New.pdf", + "2012 - Whole genome sequences of a male and female supercentenarian, ages greater than 114 years.pdf", + "2013 - Genome Instability and Aging.pdf", + "2012 - Genome-wide miRNA signatures of human longevity.pdf", + "2012 - Whole genome sequences of a male and female supercentenarian, ages greater than 114 years.pdf", + "2011 - Genome-wide association study identifies a single major locus contributing to survival into old age the APOE locus revisited.pdf", + "2017 - Genome-wide meta-analysis associates HLA.pdf" + ], + "extraction_id": [ + "8bc54e5b-f45f-54f9-9591-1e26dd80b50d", + "c918522d-c0bf-5b7a-9ced-a69d485b2cb6", + "a4aa5d3a-81e8-582c-aee6-3ebdd329de86", + "b539194c-50bb-55e5-83b2-e779f63ed363", + "402ab5b5-e6fa-58fe-8f32-7c235be7a746", + "f33756b1-7d64-5ab9-bcd6-717deaf05339", + "e79b0811-a0f3-5f44-8004-89fe59aa8a3e", + "402ab5b5-e6fa-58fe-8f32-7c235be7a746", + "a4aa5d3a-81e8-582c-aee6-3ebdd329de86", + "9c6a9e93-5dc5-571d-b3c2-b600ed95e102" + ], + "document_id": [ + "8e452186-a71c-5b62-81b2-7681c87c8e1d", + "d2a5ec28-873a-5ff3-9cf4-dbec3b52dd21", + "05208abc-5ac0-5d4d-b600-2caf59ce75b7", + "c10653f6-b3d7-5b92-9271-ab8fcc7905a7", + "408cdcd5-ab70-520a-b2c4-d9028b0a8d6f", + "71e08916-8cc8-5d96-8c06-4461b972b54d", + "18407659-c241-5f37-8ad2-ab59f6a7e288", + "408cdcd5-ab70-520a-b2c4-d9028b0a8d6f", + "05208abc-5ac0-5d4d-b600-2caf59ce75b7", + "3a565ba9-ee5b-5596-b870-ce8c055cb1f1" + ], + "id": [ + "chatcmpl-ABLwzkPUEqxCEqW5L5wugbbowvYPv", + "c2234f77-2268-57d0-a227-e931fc4802c1", + "fb0af8f1-5b2a-5ba1-8a53-ee543a9267bf", + "754929a6-af78-569a-969c-e750d174b952", + "4a6d2b9b-9496-5d90-a24a-43c643c4916b", + "1f4437a7-cee1-5dc2-80e1-9924248857d0", + "91010ff1-43a7-53f6-966d-601913e3b26b", + "63ebd662-9aca-5b8a-b3e3-89860a45da42", + "53a8e33f-da6f-5550-bf18-e45f2779f7a9", + "57227bee-d562-52c9-86dc-f9e2fcea1792", + "b1b9f731-236c-5b4b-8cc6-fcf1e06d866a" + ], + "contexts": [ + "GENOME-WIDE ASSOCIATION STUDY OF LONGEVITY 479 INCREASES in longevity of the general population world - wide are an unprecedented phenomenon with significant health and social impact. Although environmental factors have led to an increase in life span, there is ample evidence that genetic factors are involved in extreme longevity both in humans (17) and in other organisms (8). The protective genetic factors that lead to longevity are likely to involve", + "that any genetic variant that contributes strongly to extremelongevity would also be rare. One possibility is that a specificmutation could alter the protein-coding region in a gene andconfer a significant increase in longevity. Such a mutation couldact in a dominant or recessive fashion, and might be shared by asignificant fraction of the supercentenarian genomes but not bycontrol genomes. We created a computational pipeline todetermine whether our supercentenarian genomes are enrichedfor such a variant", + "ever, natural human and animal longevity is presumed to be acomplex trait (Finch & Tanzi, 1997). In humans, both candidategene and genome-wide genetic association approaches havebeen applied in an attempt to identify longevity loci. The fre-quency of genetic variants has been typically compared between nonagenarian cases and young controls, revealing", + "genetic makeup of extreme longevity is based on a combination of common and rare variants, with common vari-ants that create the background to survive to relatively common old ages, and specific combinations of uncommon and rare variants that add an additional survival advantage to even older ages. Our analy-sis showed that LAVs discovered through a casecontrol study are not necessarily the variants that make someone live to extreme old age, and additional survival analysis is needed to characterize and", + "genetic determination of human exceptional longevity, they arethe rst step toward the generation of a comprehensive referencepanel of exceptionally long-lived individuals. The data also provideinteresting insights into genetic backgrounds that are conduciveto exceptional longevity and allow us to test different models of exceptional longevity. www.frontiersin.org January 2012 | Volume 2 | Article 90 | 1", + "tremely long lived individuals. Longevity has a genetic component, with an estimated heritability of average life expectancy of approximately 25% (105, 106). Family studies of centenarians, thosewho live to 100 years or more, suggest that the relationship between genetics and longevity is stronger in the oldest-old adults (107, 108), supporting the utility of long-lived individuals as a model system for studying genetic variations that predispose people to longevity.", + "because of genetic variation that becomes particularly important for sur- vival at advanced age (Hjelmborg et al. , 2006). Epidemiological studies have revealed that long-lived individuals (LLI), that is, people surviving to the 95th percentile of the respective birth cohort-specic age distribu- tions (Gudmundsson et al. , 2000), frequently show a favorable (healthy) course of the aging process, with the absence or a delayed onset of age-", + "Studies of centenarians have provided strong evidence to sup-port the hypothesis that a genetic contribution to human excep-tional longevity is decisive, although only a small number ofgenetic variants with modest effects have been irrefutably linkedto this phenotype ( Schachter et al., 1994; Barzilai et al., 2003 ; Christensen et al., 2006 ;Wheeler and Kim, 2011 ). The tech- nology of next generation sequencing provides a tool to gen-erate data that may eventually provide an answer ( Metzker, 2009).", + "genetic contribution to human lifespan variation was estimated at 2530% in twin studies (Gudmundsson et al. , 2000; Skytthe et al. , 2003; Hjelmborg et al. , 2006). The most prominent genetic inuence is observed in families in which the capacity toattain a long lifespan clusters (Perls et al. , 2000; Schoenmaker et al. , 2006). Exceptional longevity can be reached with a low degree of age-related disability (Christensen et al. , 2008; Terry et al. , 2008), raising the question whether protective mecha-", + "age, usually de ned by a threshold, such as 90 years). Up to 25% of the variability in human lifespan has been estimated to be genetic1, but genetic variation at only three loci (near APOE , FOXO3A and CHRNA3/5 )25have so far been demonstrated to be robustly associated with lifespan. Prospective genomic studies of lifespan have been hampered by the fact that subject participation is often only recent, allowing insuf cient follow-up time for a well-powered analysis of" + ], + "answer": "Yes, there are specific genetic variations that can contribute to someone living longer. Research has shown that certain genes and their variations can influence longevity. For example, variations near the genes APOE, FOXO3A, and CHRNA3/5 have been robustly associated with lifespan [10]. These genetic variations can affect how our bodies age and how well we can avoid or delay age-related diseases. In simpler terms, think of these genes as parts of a car. Just like how certain parts can make a car run more efficiently and last longer, these genetic variations can help our bodies function better and live longer. However, it's important to note that living a long life is usually a combination of both genetic factors and lifestyle choices, such as diet, exercise, and avoiding harmful habits.", + "question": "is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert" +}
\ No newline at end of file diff --git a/gnqa/paper2_eval/src/document_operations.py b/gnqa/paper2_eval/src/document_operations.py index 0c3522f..10ed0bc 100644 --- a/gnqa/paper2_eval/src/document_operations.py +++ b/gnqa/paper2_eval/src/document_operations.py @@ -69,6 +69,7 @@ class QuestionList: #print(('', 'Level --> {0} \tDomain --> {1}\n{2}'.format(level, domain, self.print_list(query_lst))) [self._verbose]) #create_datasets(query_lst, domain, level) + def print_list(self, the_lst): ndx = 1 for item in the_lst: diff --git a/gnqa/paper2_eval/src/parse_r2r_result.ipynb b/gnqa/paper2_eval/src/parse_r2r_result.ipynb index 8ceac72..93b05c5 100644 --- a/gnqa/paper2_eval/src/parse_r2r_result.ipynb +++ b/gnqa/paper2_eval/src/parse_r2r_result.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 116, + "execution_count": 32, "metadata": {}, "outputs": [], "source": [ @@ -11,15 +11,59 @@ }, { "cell_type": "code", - "execution_count": 117, + "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "import json\n", "import sys\n", + "from document_operations import DocOps, QuestionList\n", "\n", "verbose = 0\n", - "read_file = '/data/code/gn-ai/gnqa/paper2_eval/data/rag_out_1.json'" + "read_file = '/data/code/gn-ai/gnqa/paper2_eval/data/testresp2.json'" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [], + "source": [ + "values_key = {\n", + " \"text\" : {\"name\": \"contexts\", \"append\": 1},\n", + " \"associatedQuery\": {\"name\": \"question\", \"append\": 0},\n", + " \"id\": {\"name\": \"id\", \"append\": 1},\n", + " \"title\": {\"name\": \"titles\", \"append\": 1},\n", + " \"document_id\": {\"name\": \"document_id\", \"append\": 1},\n", + " \"extraction_id\": {\"name\": \"extraction_id\", \"append\": 1},\n", + " \"content\": {\"name\": \"answer\", \"append\": 0}\n", + "}\n", + "\n", + "def get_ragas_out_dict():\n", + " return { \"titles\": [],\n", + " \"extraction_id\": [],\n", + " \"document_id\": [],\n", + " \"id\": [],\n", + " \"contexts\": [],\n", + " \"answer\": \"\",\n", + " \"question\": \"\"}\n", + "\n", + "def extract_response(obj, values_key, thedict):\n", + " if isinstance(obj, dict):\n", + " for key, val in obj.items():\n", + " if (key in values_key.keys()):\n", + " if (values_key[key][\"append\"]):\n", + " thedict[values_key[key][\"name\"]].append(val.replace(\"\\n\", \" \").strip())\n", + " else:\n", + " thedict[values_key[key][\"name\"]] = val.replace(\"\\n\", \" \").strip()\n", + " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", + " else:\n", + " if (len(obj.items()) == 1 ):\n", + " print(key, \" --> \", val)\n", + " extract_response(val, values_key, thedict)\n", + " elif isinstance(obj, list):\n", + " for item in obj:\n", + " extract_response(item, values_key, thedict)" ] }, { @@ -29,13 +73,174 @@ }, { "cell_type": "code", - "execution_count": 118, + "execution_count": 35, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "There are dict_keys(['1', '2', '3', '4', '5', '6']) keys in the result file\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwBBugt6fTuTWqXb74qvoPVubbX', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': 'The length of telomeres is significant for several reasons:\\n\\n1. **Protection of Chromosomes**: Telomeres are repetitive nucleotide sequences at the ends of eukaryotic chromosomes that protect them from attrition and damage during replication [1], [2], [6]. They prevent the loss of important genetic information and maintain genomic stability [9].\\n\\n2. **Aging and Cellular Senescence**: Telomere length is progressively shortened with each round of genomic replication unless restored by the enzyme telomerase [2], [5]. Short telomeres are considered a sign of advanced age and are associated with cellular senescence, where cells lose their ability to divide and function properly [4], [7], [8].\\n\\n3. **Disease Association**: Shorter telomeres have been linked to various diseases. For instance, individuals with Type 2 Diabetes (T2D) have been shown to have shorter leukocyte telomeres, which may be associated with disease progression [1]. Similarly, telomere length in smooth muscle cells has been linked to disease severity in atherosclerosis, and shorter leukocyte telomeres are associated with a higher risk of developing cardiovascular disease [3], [8].\\n\\n4. **Genomic Integrity**: Telomeres play a crucial role in maintaining genomic integrity and function. Shortening and erosion of telomeres can lead to chromosome end-to-end fusions and genomic instability, which can cause various cellular dysfunctions and diseases [6], [7].\\n\\n5. **Biomarker Potential**: Due to their association with aging and disease, telomere length is being studied as a potential biomarker for various health conditions, including cardiovascular diseases and diabetes [3].\\n\\nIn summary, the length of telomeres is crucial for protecting chromosomes, regulating cellular aging, and maintaining genomic stability. It also has significant implications for understanding and potentially diagnosing age-related diseases and conditions.', 'role': 'assistant'}}], 'created': 1727269299, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_e375328146', 'usage': {'completion_tokens': 387, 'prompt_tokens': 1235, 'total_tokens': 1622}}, 'search_results': {'vector_search_results': [{'id': 'bb069c10-45f1-5a83-95e3-4b7655874ba7', 'score': 0.6729372940342815, 'metadata': {'text': 'repetitive nucleotide sequences at the end of each eukaryotic chromosome, which protects them from attrition and damage. Although the relationship between leukocyte telomere length (LTL) and diabetes is still questioned\\n8, \\ndifferent studies have shown that T2D individuals have shorter leukocyte telomeres than non-T2D individuals9, 10 \\nthat may be associated with disease progression11. Indeed, the decreased antioxidant capacity described in patients', 'title': '2017 - Regular exercise participation improves genomic stability in diabetic patients an exploratory study to analyse telomere length and DNA damage.pdf', 'version': 'v0', 'chunk_order': 6, 'document_id': 'dcaf7b09-2d54-5cbf-b061-e3c4e6c6c518', 'extraction_id': '0e53122e-a308-55f7-8ee8-a0857ac9c52f', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '28e98b7e-f273-5bdd-9979-185133f311af', 'score': 0.6722932858641915, 'metadata': {'text': 'Telomeres are arrays of linked nucleotide hexamer repeats that are found at the \\nends of chromosomes in a vast clade of organisms [14]. While the sequence of \\nthese telomeric repeats can vary between organisms, their biological function is \\nhighly conserved, which is to limit damage inflicted on genes during the replica-\\ntion of chromosomes. Telomere length is progressively shortened with each round \\nof genomic replication, unless it is restored through the action of a ribonucleo-', 'title': '2020 - Clinical Genetics and Genomics of Aging.pdf', 'version': 'v0', 'chunk_order': 1510, 'document_id': '62b635c3-040e-512a-b016-6ef295308a1e', 'extraction_id': 'efd18101-9cf2-56b5-8f86-c2aba6caa0bc', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '5f940245-af1d-5eee-84dc-942017c523d0', 'score': 0.6608201462274836, 'metadata': {'text': 'telomere length,a phenomenon attributed to higher levels of oxidativestress at the cellular level (70). More recent studies havelinked telomere length in smooth muscle cells with senes-cence and disease severity in patients with atherosclero-sis (141, 150). Leukocyte telomere length was also short ina cohort of similar patients and associated with a higherrisk of developing occult cardiovascular disease (71).More data are needed to understand and validate the useof leukocyte telomere length as a biomarker', 'title': '2008 - Telomeres and Aging.pdf', 'version': 'v0', 'chunk_order': 167, 'document_id': '61d9c326-d36e-55c1-a891-335dc943e70f', 'extraction_id': '13990eb4-bef2-58ce-bf3e-0e3bc294caab', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '607cbd31-d430-5517-8212-208b25af32bf', 'score': 0.6593494015738193, 'metadata': {'text': 'age telomere length through accumulation of several short telo-\\nmeres (Londono-Vallejo et al., 2001; Martens et al., 2000) is \\nresponsible for senescence or whether a speci c chromosome \\narm limits the replication potential of human cells (Hemann et al., 2001). Individual chromosome arms were shown to have \\nlarge variations in their length (Lansdorp et al., 1996; Benn, \\n1997; Londono-Vallejo et al., 2001), and chromosome 17p seemed to be equipped with especially short telomeres in hu-', 'title': '2006 - Sex-specific telomere length profiles.pdf', 'version': 'v0', 'chunk_order': 64, 'document_id': '09c78a17-4a1f-52c1-be4d-994fd9fd71d0', 'extraction_id': '6d3bfe47-f26e-50dc-8d77-19f3797e53a0', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '53508a9e-d064-58a3-a4f9-0785470a1462', 'score': 0.6565733151606716, 'metadata': {'text': 'Telomeres are specialized structures that protect the ends of linear chromosomes. They shorten during aging due to the unidirectional activity of DNA polymerase, which leaves a section of DNA unrepli-cated on the lagging strand. Telomeres also are subject to shortening by genotoxic stress, such as oxidative damage (33). Among many eukaryotes, the enzyme telomerase maintains telomere length; but telomerase activity varies over the lifespan and between cell types, tissues, and species (34). In most human', 'title': '2018 - Sex Differences in Aging Genomic Instability.pdf', 'version': 'v0', 'chunk_order': 46, 'document_id': '8cfb5529-7f0c-58fc-b6e4-b3ee800fb72f', 'extraction_id': '396708f1-aa0a-571e-a8d3-7cb8404e9502', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '7fad29bd-12bf-53d0-af89-aadd38b974ff', 'score': 0.6563551621542922, 'metadata': {'text': 'TTAGGG sequence that cap the ends of chromosomes, protect-ing them from degradation and fusion. The length of telomererepeats is primarily maintained by active telomerase, which iscomposed of Telomerase RNA (TR) and a catalytic subunitTelomerase Reverse Transcriptase (TERT) (Blackburn, 2001).Extensive evidence has shown that telomere shortening anderosion lead to chromosome end-to-end fusions and genomicinstability (Blasco \\net al \\n., 1997; Hande \\net al \\n., 1999), causing', 'title': '2002 - Mitochondrial dysfunction leads to telomere attrition.pdf', 'version': 'v0', 'chunk_order': 6, 'document_id': 'd8bc729b-7513-58b7-b12e-0db1fb6d3b7d', 'extraction_id': 'b92ede07-74a7-524a-8d2c-54b2559e8425', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '64ef9964-1831-5a7a-8a69-5e8d0c332d37', 'score': 0.6478988125294096, 'metadata': {'text': 'a pivotal role in maintenance of genomic integrity and func-tion (Moyzis et al., 1988; McElligott and Wellinger, 1997; van \\nSteensel and de Lange, 1997). \\n It is generally accepted that telomeres shorten during DNA \\nreplication both in vitro and in vivo. In individuals, short telomeres are considered to be a sign of advanced age. Cawthon \\nand coworkers (2003) showed that telomere shortening in hu-', 'title': '2006 - Sex-specific telomere length profiles.pdf', 'version': 'v0', 'chunk_order': 5, 'document_id': '09c78a17-4a1f-52c1-be4d-994fd9fd71d0', 'extraction_id': 'eb8d8e40-a484-57cb-8125-3fd5eb3f6389', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '1b453e12-a0c4-59db-a978-bbebd689e7dc', 'score': 0.6440684007385875, 'metadata': {'text': 'Each cell division shortens telomeric DNA until, at a\\ncritical length, the cells lose capping function at thechromosomal ends, activating DNA damage check-points, cell senescence, and eventually apoptosis.Telomere shortening has particular relevance in thesetting of CVD. Leukocyte telomere length (LTL)\\nassociates signi cantly with vascular cell senescence,', 'title': '2017 - The Aging Cardiovascular System.pdf', 'version': 'v0', 'chunk_order': 61, 'document_id': 'd3ff8471-986b-5fa0-b9c4-96eaaa8fce7c', 'extraction_id': '6949970f-7bc7-5585-a57a-96de1b5ba6ec', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': '65fb74aa-f3c3-5c80-919f-329169db982f', 'score': 0.6431178642248474, 'metadata': {'text': 'nization may directly affect telomere attrition, resulting in accelerated replicative \\nsenescence and progeroid phenotypes [180].\\nTelomeres are regions constituted by tandem repeats of non-coding DNA \\nsequences 5-(TTAGGG)n-3 and a protein complex called shelterin, bound to them. \\nThis structure ensures the stability of the genome and protects the chromosomes \\nfrom a wrong action of the DNA repair machinery [184] by allowing the formation \\nof a chromatin loop called T-Loop [185].', 'title': '2020 - Clinical Genetics and Genomics of Aging.pdf', 'version': 'v0', 'chunk_order': 1084, 'document_id': '62b635c3-040e-512a-b016-6ef295308a1e', 'extraction_id': 'd4afa45a-5efa-577b-822e-7a82c2f6508d', 'associatedQuery': 'What is the significance of the length of telomeres?'}}, {'id': 'f181e6da-58b6-5f26-87a2-355e25388673', 'score': 0.6414439869357347, 'metadata': {'text': 'telomeres, the repetitive sequence at the end of linear chromosomes, has garnered much attention for\\nits relation to aging. Telomere repeats serve as an internal clock for cycling cells because each round of\\nreplication results in the loss of telomeric DNA in the absence of active telomerase (reviewed in [66]).\\nEventually, this loss over cellular generations culminates in telomere crisis and a permanent state of', 'title': '2018 - Repetitive Fragile Sites Centromere Satellite DNA.pdf', 'version': 'v0', 'chunk_order': 35, 'document_id': '262df0d6-ad68-544a-88ed-b4568f305858', 'extraction_id': '3b0cb0ab-421d-54d7-9816-c6a2e6f1ac68', 'associatedQuery': 'What is the significance of the length of telomeres?'}}], 'kg_search_results': None}}\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "domain_expoert_aging_1\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwRFLcOLGvXJuXhHs6NCge9tY7Z', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': 'The mouse genes associated with longevity include:\\n\\n1. **Mouse loci associated with life span**: These loci exhibit sex-specific and epistatic effects [1].\\n2. **Mouse growth hormone receptor**: Alterations in this gene result in increased lifespan [3], [4].\\n3. **Lmna heterozygosity**: This genetic modification ameliorates progeroid phenotypes and extends lifespan [6].\\n\\nThese references provide evidence of specific genes and loci in mice that have been linked to increased longevity.', 'role': 'assistant'}}], 'created': 1727269315, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_e375328146', 'usage': {'completion_tokens': 103, 'prompt_tokens': 1413, 'total_tokens': 1516}}, 'search_results': {'vector_search_results': [{'id': '09da6f9e-b996-5438-91be-41d9438cb930', 'score': 0.7879571445013809, 'metadata': {'text': '11. Gelman R, Watson A, Bronson R et al (1988) Murine chromo-\\nsomal regions correlated with longevity. Genetics\\n118(4):693704\\n12. Jackson AU, Galecki AT, Burke DT et al (2002) Mouse loci\\nassociated with life span exhibit sex-specic and epistatic effects.\\nJ Gerontol A Biol Sci Med Sci 57(1):B9B15\\n13. Foreman JE, Lionikas A, Lang DH et al (2009) Genetic archi-\\ntecture for hole-board behaviors across substantial time intervalsin young, middle-aged and old mice. Genes Brain Behav', 'title': '2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf', 'version': 'v0', 'chunk_order': 67, 'document_id': 'ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b', 'extraction_id': '5cc56e3b-53ab-5299-814d-014e2ed31d2f', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '14bf5e8a-4095-536f-b98b-00c8cdae3a31', 'score': 0.7488234639167786, 'metadata': {'text': 'Long-lived rodents reveal signatures of positive selection in genes associated\\nwith lifespan. PLoS Genet. 14:e1007272. doi: 10.1371/journal.pgen.100\\n7272\\nSchchter, F., Faure-Delanef, L., Gunot, F., Rouger, H., Froguel, P., Lesueur-Ginot,\\nL., et al. (1994). Genetic associations with human longevity at the APOE and\\nACE loci. Nat. Genet. 6, 2932. doi: 10.1038/ng0194-29\\nSchinaman, J. M., Rana, A., Ja, W. W., Clark, R. I., and Walker, D. W. (2019).', 'title': '2021 - Footprints in the Sand Deep Taxonomic Comparisons in Vertebrate Genomics to Unveil the Genetic Programs of Human Longevity.pdf', 'version': 'v0', 'chunk_order': 137, 'document_id': '0dc45abe-ab02-5b07-9916-7093b53323c0', 'extraction_id': '11ca91fa-a13f-5cc5-90c8-53d1ebe76836', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': 'f8fdd2ee-710c-5d2c-8a70-bf48f4927653', 'score': 0.7425085306167603, 'metadata': {'text': 'of the mouse growth hormone receptor results in severely decreased body weights, insulin, and insulin- like \\ngrowth factor I levels and increased life span. Endocrinology 144:37993810. DOI: https://doi.org/10.1210/en. \\n2003-0374, PMID: 12933651\\nde Haan G, Williams RW. 2005. A genetic and genomic approach to identify longevity genes in mice. \\nMechanisms of Ageing and Development 126:133138. DOI: https://doi.org/10.1016/j.mad.2004.09.012, \\nPMID: 15610771', 'title': '2021 - Genetic loci and metabolic states associated with murine epigenetic aging.pdf', 'version': 'v0', 'chunk_order': 224, 'document_id': 'b82bd9e1-2373-577b-a942-164565eaca6b', 'extraction_id': 'a9ebf1d8-5ef8-5c52-962e-110873476823', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': 'e613d3df-adb0-56b0-abfd-8828020c23c3', 'score': 0.7425085306167603, 'metadata': {'text': 'of the mouse growth hormone receptor results in severely decreased body weights, insulin, and insulin- like \\ngrowth factor I levels and increased life span. Endocrinology 144:37993810. DOI: https://doi.org/10.1210/en. \\n2003-0374, PMID: 12933651\\nde Haan G, Williams RW. 2005. A genetic and genomic approach to identify longevity genes in mice. \\nMechanisms of Ageing and Development 126:133138. DOI: https://doi.org/10.1016/j.mad.2004.09.012, \\nPMID: 15610771', 'title': '2021 -Mozhui- Epigenetic aging.pdf', 'version': 'v0', 'chunk_order': 224, 'document_id': 'd23daa43-4176-54e6-b3c3-b889843e92f1', 'extraction_id': 'e662d80d-b529-5749-856c-ed734c6e3eaa', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '02296a91-f1a4-5b35-a5d1-e1851797404b', 'score': 0.7411562954690294, 'metadata': {'text': 'Mulvey L, Sinclair A, Selman C (2014) Lifespan modulation in mice\\nand the confounding effects of genetic background. J Genet\\nGenomics 41:497503. doi: 10.1016/j.jgg.2014.06.002\\nOConnor TP, Lee A, Jarvis JUM, Buffenstein R (2002) Prolonged\\nlongevity in naked mole-rats: age-related changes in metabolism,\\nbody composition and gastrointestinal function. Comp Biochem\\nPhysiol A 133:835842. doi: 10.1016/S1095-6433(02)00198-8\\nOpazo JC, Palma RE, Melo F, Lessa EP (2005) Adaptive evolution of', 'title': '2016 - Unraveling the message insights into comparative genomics.pdf', 'version': 'v0', 'chunk_order': 188, 'document_id': '0deba7bb-c27a-5d9e-b1b2-e48a5574882c', 'extraction_id': 'c6f50e80-1bc5-5b0a-b57b-4c2bfe524d96', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '90214d4d-4068-5490-9049-5604b5dcf3e2', 'score': 0.7377414547050879, 'metadata': {'text': '/ mice by Lmna heterozy-\\ngosity ameliorates progeroid phenotypes and extends \\nlifespan [143, 174, 175].', 'title': '2012 - Chromatin Remodeling, DNA Damage Repair and Aging.pdf', 'version': 'v0', 'chunk_order': 112, 'document_id': '594e5dbe-b92a-5b0c-9f65-2a10670f9517', 'extraction_id': 'd9a12bd9-c65e-547a-89aa-4e0231558ddc', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '56e03e38-0ae5-5b29-b929-662fa091e0ac', 'score': 0.7320996842265558, 'metadata': {'text': 'References\\n1. Hook Met al.Genetic cartography of longevity in humans and mice: Current landscape and horizons. \\nBiochim. Biophys. Acta1864, 27182732 (2018).\\n2. Kuningas Met al.Genes encoding longevity: from model organisms to humans. Aging Cell7, 270\\n280 (2008). [PubMed: 18208581] \\n3. de Magalhes JP, Wuttke D, Wood SH, Plank M & V ora C Genome-environment interactions that \\nmodulate aging: Powerful targets for drug discovery. Pharmacol. Rev. 64, 88101 (2012). [PubMed: \\n22090473]', 'title': '2021 - Gene-by-environment modulation of lifespan and weight gain in the murine BXD family.pdf', 'version': 'v0', 'chunk_order': 130, 'document_id': '4d082da4-fa48-5170-8147-c4fea47a5d4b', 'extraction_id': '30ba3324-6e19-58c2-9e32-508f827af3e5', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': 'ebc5b444-a63f-5819-9d3a-ffbf96b3d367', 'score': 0.7316716909408569, 'metadata': {'text': '\"Murine chromosomal regions correlated with longevity.\" Genetics 118: 693-704.', 'title': '2006 - THE GENETIC REGULATION OF THE RESPONSE OF HEMATOPOIETIC STEM_PROG.pdf', 'version': 'v0', 'chunk_order': 381, 'document_id': 'b84914bc-195d-5c48-8e89-0db719675c1f', 'extraction_id': 'c04cac81-a0b0-5d0a-b21e-2f94494bb302', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '80d01818-7573-5321-b33d-c7e291f3fe74', 'score': 0.7243530750274658, 'metadata': {'text': 'expression of alpha-1,2-mannosidase I extends lifespan in \\nDrosophila melanogaster and Caenorhabditis elegans . Aging Cell, \\n2009 , 8(4), 370-9. \\n[73] Wang, H.D.; Kazemi-Esfarjani, P.; Benzer, S. Multiple-stress \\nanalysis for isolation of Drosophila longevity genes . Proc Natl \\nAcad Sci U S A , 2004 , 101(34), 12610-5. \\n[74] Lin, Y.J.; Seroude, L.; Benzer, S. Extended life-span and stress \\nresistance in the Drosophila mutant methuselah . Science , 1998 , \\n282(5390), 943-6.', 'title': '2012 - Genome-Scale Studies of Aging Challenges and Opportunities.pdf', 'version': 'v0', 'chunk_order': 91, 'document_id': 'b77aace0-fa36-5fd4-8e2a-c8932198acd1', 'extraction_id': '9669b6fe-e9d7-55e8-a91a-c015df633daa', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}, {'id': '11af155f-85c6-5f8b-8943-5391ad678f7e', 'score': 0.7239880130298143, 'metadata': {'text': 'sion analysis of mouse liver genes: effect of age and of thelongevity mutant Prop1df. J Gerontol A Biol Sci Med Sci 56:\\nB72B80, 2001.\\n12.Fabrizio P, Pozza F, Pletcher SD, Gendron CM, and Longo\\nVD. Regulation of longevity and stress resistance by Sch9 in\\nYeast. Science 292: 288 290, 2001.\\n13.Haase D, Lehmann MH, Korner MM, Korfer R, Sigusch\\nHH, and Figulla HR. Identi cation and validation of selective', 'title': '2003 - Lifelong voluntary exercise in the mouse prevents.pdf', 'version': 'v0', 'chunk_order': 141, 'document_id': '24d4f270-f45b-5830-84f9-b1e5bcd3c070', 'extraction_id': '6a2cdf66-f3c9-5be9-b6b0-f203be169103', 'associatedQuery': 'Which mouse genes have been associated with longevity?'}}], 'kg_search_results': None}}\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "domain_expoert_aging_2\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwW9HA9VG184zgOmenEBU2eMIMc', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': 'Genetic factors associated with aging include:\\n\\n1. **Genome-wide association studies (GWAS)**: These studies offer an unbiased approach to identify new candidate genes for human diseases, including those related to aging. Convergent results from multiple aging-related traits can point out the genes responsible for the general aging of the organism [2].\\n\\n2. **Longevity-associated genes**: Dozens of genes have been associated with human longevity, although only a handful have shown consistent effects across populations. These genes are often related to specific biological pathways and processes [4].\\n\\n3. **Genes involved in mitochondrial and proteasomal functions**: Aging is associated with alterations in the transcript levels of many genes, including those involved in evolutionarily conserved mitochondrial and proteasomal functions. Some of these genes have been shown to be directly involved in regulating lifespan [7].\\n\\n4. **Genes with protective functions**: Certain genes that are overexpressed with age seem to have protective functions, helping organisms manage aging. These genes could be targets for manipulation to potentially influence the aging process [8].\\n\\nThese genetic factors highlight the complex interplay of various genes and pathways in the aging process.', 'role': 'assistant'}}], 'created': 1727269320, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_e375328146', 'usage': {'completion_tokens': 231, 'prompt_tokens': 1014, 'total_tokens': 1245}}, 'search_results': {'vector_search_results': [{'id': '3117c019-7311-53ae-8ab1-927ca822c709', 'score': 0.7238354898642153, 'metadata': {'text': 'It is undisputed that genetic factors influence aging. In a remarkable', 'title': '2009 - The Human Ageing Genomic Resources online.pdf', 'version': 'v0', 'chunk_order': 9, 'document_id': 'e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529', 'extraction_id': '7ada6b55-99c2-5e20-bf96-d153f927256c', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '0ad664d2-6756-5123-b192-8a56cf6887a5', 'score': 0.7047669643441531, 'metadata': {'text': 'perform a study of the genetic sources of biological\\naging. However, to be successful, the genetic study of acomplex condition requires a heritable phenotype to be\\ndeveloped and validated. Genome-wide association\\nstudies offer an unbiased approach to identify newcandidate genes for human diseases. It is hypothesized\\nthat convergent results from multiple aging-related traits\\nwill point out the genes responsible for the general agingof the organism. This perspective focuses on the', 'title': '2011 - How pleiotropic genetics of the musculoskeletal system.pdf', 'version': 'v0', 'chunk_order': 1, 'document_id': 'ed31486c-a651-5894-bd96-21fbd78f2646', 'extraction_id': 'b5b3c74a-90de-5b1e-9580-8031b10be7ec', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '9fa00091-9661-57bd-91c7-f0bf436805a7', 'score': 0.7019733190536499, 'metadata': {'text': 'population dynamics on the genetic architecture of human longevity. Aging (Albany NY). 2018;10(8):1947 63.\\n68. Bellenguez C, Kucukali F, Jansen I, Andrade V, Morenau-Grau S, Amin N, et al. Large meta-analysis of genome-wide\\nassociation studies expands knowledge of the genetic etiology of Alzheimer disease and highlights potential\\ntranslational opportunities. medRxiv. 2020.\\n69. Kojima T, Shimazui T, Hinotsu S, Joraku A, Oikawa T, Kawai K, et al. Decreased expression of CXXC4 promotes a', 'title': '2021 - Genome-wide association studies identify.pdf', 'version': 'v0', 'chunk_order': 192, 'document_id': '60c2e869-1fee-53ea-b332-26d9c2abc747', 'extraction_id': 'cd7730b6-22dc-5256-9310-79fc348b3226', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '786d2756-4c4d-5ac0-8d3d-63f914d51664', 'score': 0.6959169273475545, 'metadata': {'text': 'In addition to aging- and CR-related genes, another\\nsource of candidate genes and pathways for drug designare human longevity-associated genes (Barzilai andShuldiner, 2001; Browner et al., 2004; Kenyon, 2010).Dozens of genes have now been associated with humanlongevity (de Magalha es et al., 2009a), although only ahandful of genes have been shown to have consistenteffects across populations.\\nMany longevity-associated genes are related to spe-', 'title': '2012 - Genome-Environment Interactions That Modulate.pdf', 'version': 'v0', 'chunk_order': 119, 'document_id': 'b1a1997c-e9df-5dc0-9d12-a3977d0c64ec', 'extraction_id': 'd59d7882-333d-5576-86ab-3cfa6354b946', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': 'a0672677-71ad-5603-8427-a0648eec407f', 'score': 0.6954198479652405, 'metadata': {'text': 'Clinical Genetics and Genomics of Aging', 'title': '2020 - Clinical Genetics and Genomics of Aging.pdf', 'version': 'v0', 'chunk_order': 1, 'document_id': '62b635c3-040e-512a-b016-6ef295308a1e', 'extraction_id': '4ea8424f-1cd8-569c-a1df-3f0f54206e70', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': 'e0cce1c5-8709-5218-99b6-48a6ba242931', 'score': 0.694896936416626, 'metadata': {'text': 'effect fundamental mechanisms of aging (14, 16). The drawbacksof such studies include the improbability of picking the right geneto study the myriad of known and unknown genes affecting theprocess of interest (17). The linkage study described heremarkedly improves the efficiency of such association studies bydefining a region likely to contain polymorphism(s) with signif-icant influence on life span.\\nAdditional association studies with these families and repli-', 'title': '2001 - A genome-wide scan for linkage to human.pdf', 'version': 'v0', 'chunk_order': 40, 'document_id': '1431984a-82d9-51d4-a23c-5f76a02ab554', 'extraction_id': '17246c43-2e44-579b-867d-3dc7150ceedd', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': 'bf2cd208-273f-5848-b243-df8b95ea7833', 'score': 0.6911037152347747, 'metadata': {'text': 'The multifactorial and temporal features of aging can beanalyzed efficiently by genome-wide transcriptional profiling,which has been conducted in various model organisms and hu-mans (Melov and Hubbard 2004). Aging is associated with alter-ations in transcript levels of many genes, including those in-volved in evolutionarily conserved mitochondrial and protea-somal functions (McCarroll et al. 2004), some of which havebeen shown to be directly involved in regulating lifespan in C.', 'title': '2007 - Temporal and spatial transcriptional profiles.pdf', 'version': 'v0', 'chunk_order': 11, 'document_id': '38f27ec7-08bf-5397-b2b8-bde95e0dc3f8', 'extraction_id': '2e42619b-d0b2-5d33-aab8-6f04002ee807', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '413f8f54-b5cc-5089-9f5c-d9e3b8bcf594', 'score': 0.6904207652556452, 'metadata': {'text': 'overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,', 'title': '2012 - Genome-Environment Interactions That Modulate.pdf', 'version': 'v0', 'chunk_order': 114, 'document_id': 'b1a1997c-e9df-5dc0-9d12-a3977d0c64ec', 'extraction_id': 'd59d7882-333d-5576-86ab-3cfa6354b946', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '50581d4f-396c-5d12-aec6-5f42e2ab88ef', 'score': 0.6901622229911234, 'metadata': {'text': 'Mol Genet Genomic Med. 2020;00:e1157. | 1 of 11\\nhttps://doi.org/10.1002/mgg3.1157\\nwileyonlinelibrary.com/journal/mgg3\\n1 | INTRODUCTION\\nAging is one of the inevitably dominant risk associated with \\nmany diseases.\\nSeveral biological factors contribute to this etiology which', 'title': '2020 - Role of Helicobacter pylori infection in the manifestation of old age-related diseases.pdf', 'version': 'v0', 'chunk_order': 0, 'document_id': 'e99c68d2-4f35-5591-8072-cfdb31966e68', 'extraction_id': 'e6916baa-9f9d-57aa-b44d-95fb614610a8', 'associatedQuery': 'what genetic factor are associated with aging'}}, {'id': '3c369292-4b9c-5156-a80f-4b3301026f30', 'score': 0.6883950233459473, 'metadata': {'text': 'al., 2009; Stanfel et al., 2009). Many of these genesmodulate the response to environmental signals, such asfood availability, and act in signaling pathways that ifunderstood can be targeted (Fig. 1). The genetic regula-tion of aging is therefore an emerging field with multipleapplications in the human nutrition, cosmetic, and phar-maceutical industries.\\nAGING GENES AS TARGETS FOR DRUG DISCOVERY 91', 'title': '2012 - Genome-Environment Interactions That Modulate.pdf', 'version': 'v0', 'chunk_order': 67, 'document_id': 'b1a1997c-e9df-5dc0-9d12-a3977d0c64ec', 'extraction_id': 'a01ca925-4ccf-5863-a162-7bd4c754fe89', 'associatedQuery': 'what genetic factor are associated with aging'}}], 'kg_search_results': None}}\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", "\n", "\n", "\n", @@ -67,6 +272,8 @@ "\n", "\n", "\n", + "domain_expoert_aging_3\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwhCwS1z9hZBn1zWSbHm5JcD7CF', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': 'Genes typically associated with early aging include those involved in segmental progeroid syndromes, such as the Werner syndrome gene [2]. Additionally, genes critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway, are also associated with early aging [2].', 'role': 'assistant'}}], 'created': 1727269331, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_e375328146', 'usage': {'completion_tokens': 58, 'prompt_tokens': 1277, 'total_tokens': 1335}}, 'search_results': {'vector_search_results': [{'id': 'b719fbc0-94e4-5df0-abb7-0d13fc36214c', 'score': 0.7486875952854639, 'metadata': {'text': 'lar signatures of mammalian aging. Some of the genes', 'title': '2012 - Genome-Environment Interactions That Modulate.pdf', 'version': 'v0', 'chunk_order': 113, 'document_id': 'b1a1997c-e9df-5dc0-9d12-a3977d0c64ec', 'extraction_id': 'd59d7882-333d-5576-86ab-3cfa6354b946', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb', 'score': 0.7380977429093288, 'metadata': {'text': 'www.ncbi.nlm.nih.gov/homologene) of genes strongly asso-ciated with aging in model organisms. Also included are genesin which mutations result in segmental progeroid syndromes,such as the Werners syndrome gene, as well as genes criticalin pathways previously related to aging, such as the insulin/insulin-like signalling pathway (de Magalhes \\net \\n \\nal \\n., 2005a). The', 'title': '2009 - The Human Ageing Genomic Resources online.pdf', 'version': 'v0', 'chunk_order': 18, 'document_id': 'e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529', 'extraction_id': '52c67b46-63f2-54ae-a78e-e9d54a55f6e4', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '413f8f54-b5cc-5089-9f5c-d9e3b8bcf594', 'score': 0.7369449452227419, 'metadata': {'text': 'overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,', 'title': '2012 - Genome-Environment Interactions That Modulate.pdf', 'version': 'v0', 'chunk_order': 114, 'document_id': 'b1a1997c-e9df-5dc0-9d12-a3977d0c64ec', 'extraction_id': 'd59d7882-333d-5576-86ab-3cfa6354b946', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '896169ed-4b9b-5ebc-9c9d-1cd2e6f3437c', 'score': 0.7291975344184, 'metadata': {'text': 'expression profile of aging in human muscle. Physiol Genomics\\n2003;14:149-59.\\n142.\\nRodwell GE, Sonu R, Zahn JM. A transcriptional profile of aging inthe human kidney. PLoS Biol 2004;e427:2.\\n143. Hasty P, Campisi J, Hoeijmakers J, van Steeg H, Vijg J. Aging and\\ngenome maintenance: lessons from the mouse? Science 2003;299:1355-9.\\n144. Kyng KJ, May A, Klvraa S, Bohr VA. Gene expression profiling in\\nWerner syndrome closely resembles that of normal aging. Proc Natl\\nAcad Sci U S A 2003;100:12259-64.', 'title': '2011 - Clinical aspects and molecular diagnostics of skin aging.pdf', 'version': 'v0', 'chunk_order': 149, 'document_id': 'e32f8f2c-d3ad-5dae-a393-9bd87c370ebe', 'extraction_id': '674e1da7-73d5-5101-b5a5-4981e483123c', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '6b4fb407-fd3f-52a3-9cfd-07dc5c891dd5', 'score': 0.7250815197776855, 'metadata': {'text': 'neurodegenerative diseases. Nature. 2006;443:787 95.\\n50. de Magalhes JP, Curado J, Church GM. Meta-analysis of age-related gene\\nexpression profiles identifies common signatures of aging. Bioinformatics.\\n2009;25:875 81.\\n51. Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, et al. AGEMAP:\\na gene expression database for aging in mice. PLoS Genet. 2007;3:e201.\\n52. Liu LF, Shen WJ, Ueno M, Patel S, Kraemer FB. Characterization of age-\\nrelated gene expression profiling in bone marrow and epididymal', 'title': '2015 - Transcriptomic profiles of aging in purified.pdf', 'version': 'v0', 'chunk_order': 172, 'document_id': '50f357a3-e0f2-5e32-a6b2-771fb4b1e1c6', 'extraction_id': 'e5fd1ff0-8df5-577f-9f2d-31b0941d5ce5', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '17ce11f7-55df-59bd-a801-a6f38ae9a9ef', 'score': 0.7242769763304618, 'metadata': {'text': 'Ly DH, Lockhart DJ, Lerner RA, Schultz PG (2000) Mitotic misregulation and\\nhuman aging. Science 287: 24862492.\\nMcCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, et al. (2004)\\nComparing genomic expression patterns across species identies shared\\ntranscriptional prole in aging. Nat Genet 36: 197204.\\nMurphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, et al. (2003)\\nGenes that act downstream of DAF-16 to inuence the lifespan of\\nCaenorhabditis elegans Nature 424: 277283.', 'title': '2004 - A Transcriptional Profile of Aging.pdf', 'version': 'v0', 'chunk_order': 155, 'document_id': '4ab656a7-9656-526b-94e1-422875409b44', 'extraction_id': '8b47c304-ee91-5c52-8324-79fd0bd32b27', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '61baeaa5-d65a-54b5-bfee-9bab8bbf1985', 'score': 0.7208183740593941, 'metadata': {'text': 'genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence\\ntend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and\\ntumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes.\\nFurthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build', 'title': '2020 - A multidimensional systems biology.pdf', 'version': 'v0', 'chunk_order': 2, 'document_id': 'd040bfe3-e409-5b5c-b8f8-f3dd4fc060e3', 'extraction_id': '9d1656aa-32d2-5094-8232-4817655b1cbd', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '3414ff44-7d60-5492-9956-353ab9a94a43', 'score': 0.719908313756687, 'metadata': {'text': 'exhibits important alterations in global gene expressionproles with age. In mice, aging is accompanied by changesin expression of genes associated with increased inamma-tion, cellular stress, brosis, altered capacity for apoptosis,xenobiotic metabolism, normal cell-cycle control, and DNAreplication [ 5]. Lifelong calorie restriction reversed the', 'title': '2011 - Metabolism, Genomics, and DNA Repair in the Mouse Aging Liver.pdf', 'version': 'v0', 'chunk_order': 9, 'document_id': 'a94fd15d-373e-51c5-ad74-a17e4260d32a', 'extraction_id': 'a6a6b5ba-3a72-55c5-91bb-abe747624348', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': 'b2d47567-09dc-5c77-be72-9448aa954e6b', 'score': 0.7168636322021535, 'metadata': {'text': 'stance, genes associated with energy production, which decrease\\ntheir expression during aging across various tissues and species\\n(Zahn et al. 2006, 2007; de Magalha es et al. 2009), start decreasing\\nat this transition point in our data (group 5; Fig. 2A). Hence, 25 yr\\nof age in humans may mark the beginning of systemic change\\nassociated with certain senescence processes.\\nConservation of expression changes with age\\nWe observe that both developmental and aging expression pro-', 'title': '2010 - MicroRNA, mRNA, and protein expression link.pdf', 'version': 'v0', 'chunk_order': 85, 'document_id': 'c3ae47b0-42dd-5ab0-8fec-a41831d1bbfa', 'extraction_id': 'fc9974c9-2e48-5a08-9112-0109df9ce096', 'associatedQuery': 'which genes are typically associated with early aging?'}}, {'id': '1c3f7772-e1fa-5063-bda7-04b2f7e7b0e3', 'score': 0.715810554277269, 'metadata': {'text': 'p <10\\n-6; Table 1 shows the top 25 genes. Many of these\\ngenes have been associated with age-related diseases.Several other genes that have been shown to play a role\\nin aging such as lysosomal-associated membrane\\nprotein-2 Lamp2 [19] (p = 5.68\\n-30), Fas [20] (p = 2.70-31)\\nand growth hormone receptor Ghr [21] (p = 1.34-19) also\\nshowed a significant co-expression. Anxa2, Anxa3 and\\nAnxa4 also show a low p-value (p < 10-25) as well as\\nseveral S100 calcium binding proteins which have been', 'title': '2012 - GeneFriends An online co-expression analysis.pdf', 'version': 'v0', 'chunk_order': 27, 'document_id': 'be20af52-c782-5098-893a-9a92000bf5a0', 'extraction_id': '1839dfa6-7080-5de4-96cb-3493ca2056d3', 'associatedQuery': 'which genes are typically associated with early aging?'}}], 'kg_search_results': None}}\n", "\n", "\n", "\n", @@ -96,60 +303,191 @@ "\n", "\n", "\n", - "\n" + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "domain_expoert_aging_4\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwlxjoJ15UXMdKPBfDnYfvZNLDD', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': 'To generate a linkage or association mapping study in mice to understand aging, you can follow these steps:\\n\\n1. **Select Appropriate Mouse Strains**: Choose inbred mouse strains that are known to have variations in lifespan and aging-related traits. Inbred strains are powerful for identifying genes underlying complex traits such as longevity due to their genetic uniformity [9].\\n\\n2. **Identify Aging-Related Traits**: Determine the specific aging-related traits you want to study. This could include longevity, resistance to age-associated diseases, or other biomarkers of aging [4].\\n\\n3. **Cross Mouse Strains**: Perform crosses between different inbred strains to generate F1 and F2 generations. This helps in creating genetic diversity necessary for mapping studies [5].\\n\\n4. **Phenotyping**: Assay the F2 generation (or other relevant generations) for the aging-related traits of interest. This could involve measuring lifespan, resistance to diseases, or other biomarkers [4].\\n\\n5. **Genotyping**: Genotype the mice using molecular markers such as SNPs (Single Nucleotide Polymorphisms) to identify genetic variations across the genome [6].\\n\\n6. **Quantitative Trait Locus (QTL) Mapping**: Use QTL mapping techniques to identify chromosomal regions associated with the aging-related traits. This involves statistical analysis to correlate genetic markers with phenotypic traits [6].\\n\\n7. **Association Studies**: Conduct association studies to further refine the regions identified by QTL mapping. This involves looking for specific polymorphisms within the identified regions that are significantly associated with the traits [1].\\n\\n8. **Replication and Validation**: Validate the findings by replicating the study in different mouse populations or using additional genetic crosses. This helps to confirm the association between the identified genetic regions and aging traits [1].\\n\\nBy following these steps, you can generate a linkage or association mapping study in mice to understand the genetic factors influencing aging.', 'role': 'assistant'}}], 'created': 1727269335, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_3537616b13', 'usage': {'completion_tokens': 387, 'prompt_tokens': 1231, 'total_tokens': 1618}}, 'search_results': {'vector_search_results': [{'id': 'e0cce1c5-8709-5218-99b6-48a6ba242931', 'score': 0.7081564664840698, 'metadata': {'text': 'effect fundamental mechanisms of aging (14, 16). The drawbacksof such studies include the improbability of picking the right geneto study the myriad of known and unknown genes affecting theprocess of interest (17). The linkage study described heremarkedly improves the efficiency of such association studies bydefining a region likely to contain polymorphism(s) with signif-icant influence on life span.\\nAdditional association studies with these families and repli-', 'title': '2001 - A genome-wide scan for linkage to human.pdf', 'version': 'v0', 'chunk_order': 40, 'document_id': '1431984a-82d9-51d4-a23c-5f76a02ab554', 'extraction_id': '17246c43-2e44-579b-867d-3dc7150ceedd', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '9f9fef49-0bda-5948-93bd-0f8f43bbefdf', 'score': 0.6985010712892139, 'metadata': {'text': 'Map contains 1119 and 1459 curated human and mouse aginggenes, respectively, covering almost all scales of aging, rangingfrom molecular damage to genetic predisposition. Cross-speciescomparison revealed a modest overlap between known humanand mouse aging genes, suggesting both conservation of core sen-\\nescence pathways and fundamental differences in aging between\\nmice and humans (Fig. 2E).\\nAging-associated genes can alternatively be identified in a', 'title': '2023 - A transcriptome-based single-cell biological age model.pdf', 'version': 'v0', 'chunk_order': 32, 'document_id': '9be234b7-f37d-5cd5-8895-bfe676441b2f', 'extraction_id': '0fd46f00-d3e1-54f4-9395-6c3e8294ed51', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '09da6f9e-b996-5438-91be-41d9438cb930', 'score': 0.6970219196664155, 'metadata': {'text': '11. Gelman R, Watson A, Bronson R et al (1988) Murine chromo-\\nsomal regions correlated with longevity. Genetics\\n118(4):693704\\n12. Jackson AU, Galecki AT, Burke DT et al (2002) Mouse loci\\nassociated with life span exhibit sex-specic and epistatic effects.\\nJ Gerontol A Biol Sci Med Sci 57(1):B9B15\\n13. Foreman JE, Lionikas A, Lang DH et al (2009) Genetic archi-\\ntecture for hole-board behaviors across substantial time intervalsin young, middle-aged and old mice. Genes Brain Behav', 'title': '2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf', 'version': 'v0', 'chunk_order': 67, 'document_id': 'ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b', 'extraction_id': '5cc56e3b-53ab-5299-814d-014e2ed31d2f', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': 'ab0845d4-b4db-53db-927e-b96a52cf7667', 'score': 0.694593608379364, 'metadata': {'text': 'Along with longevity, a select group of potential aging-related biomarkers will be assayed for each of these mouse models. In addition, it should be possible to assay several of these mouse lines for resistance to specific age-associated diseases, such as diabetes and neurological disorders, by \\ncrossing them into the appropriate transgenic disease back-\\nground. \\nCONCLUSION \\n Our understanding of the basic mechanisms of aging \\nhave benefited greatly from the use of simple model systems', 'title': '2007 - Longevity Genomics Across Species.pdf', 'version': 'v0', 'chunk_order': 50, 'document_id': '1ab0b63f-d97c-5f5c-98ee-0bde785fa630', 'extraction_id': '522e2616-daa1-5bf3-8673-a717dfb9b13f', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': 'c2299f0f-9e0b-5279-90e5-37c6bd664976', 'score': 0.6905311346054077, 'metadata': {'text': '198\\nthe study of age-related diseases for various reasons: (a) mice are closely related to \\nhumans, with nearly 99% of human orthologous in mice; (b) their relatively short \\nlifespan and small size allow surveillance of the aging process within a pertinent \\ntime frame and make their housing less expensive; (c) the feasibility of performing \\ngenetic manipulations facilitates the engineering of transgenic strains (gain- and \\nloss-of function mice) that model premature aging disorders. In this section, we', 'title': '2020 - Clinical Genetics and Genomics of Aging.pdf', 'version': 'v0', 'chunk_order': 1366, 'document_id': '62b635c3-040e-512a-b016-6ef295308a1e', 'extraction_id': '5c3840bd-45a5-5928-84ab-a1f2d8536691', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '3004d1fd-c5ce-5587-bfab-471e7141952c', 'score': 0.6893202477288406, 'metadata': {'text': 'Hsu HC, Lu L, Yi N, Van Zant G, Williams RW, Mountz JD. Quantitative trait locus (QTL) mapping in \\naging systems. Methods in Molecular Biology (Clifton, NJ ). 2007; 371:321348.\\nHunter KW, Crawford NPS. The future of mouse QTL mapping to diagnose disease in mice in the age \\nof whole-genome association studies. Annual Review of Genetics. 2008; 42:131141.\\nIto R, Robbins TW, Everitt BJ. Differential control over cocaine-seeking behavior by nucleus', 'title': '2017 - Systems genetic analysis in GeneNetwork.org.pdf', 'version': 'v0', 'chunk_order': 114, 'document_id': '41be0f9f-a5af-5586-b6cd-16e56fd89cdc', 'extraction_id': '59121146-02b9-5479-96e2-9fb45cffc81b', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '9082d164-59f8-58a0-ace7-8b3aa9d884e2', 'score': 0.6867029666900635, 'metadata': {'text': 'multiscalar integration of traits. Cell150, 12871299 (2012). [PubMed: 22939713] \\n33. De Haan G & Van Zant G Genetic analysis of hemopoietic cell cycling in mice suggests its \\ninvolvement in organismal life span. FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol. 13, 707713 \\n(1999).\\n34. Gelman R, Watson A, Bronson R & Yunis E Murine chromosomal regions correlated with \\nlongevity. Genetics 118, 693704 (1988). [PubMed: 3163317] \\n35. Houtkooper RHet al.The metabolic footprint of aging in mice. Sci. Rep1, (2011).', 'title': '2021 - Gene-by-environment modulation of lifespan and weight gain in the murine BXD family.pdf', 'version': 'v0', 'chunk_order': 142, 'document_id': '4d082da4-fa48-5170-8147-c4fea47a5d4b', 'extraction_id': '396683f9-b2e3-5942-bec8-f96fa798c341', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '7abf14d2-cdfe-5c37-8217-6b63bd8fb255', 'score': 0.6810372471809387, 'metadata': {'text': 'mice to identify genetic factors involved in the regulation of\\ncognitive aging that may have gone undetected in either complex\\nhuman studies or murine studies utilizing only a single genetic\\nbackground. Aging is a leading risk factor for age-associated de-\\nmentias such as AD, and our work and others suggest that geneticfactors and mechanisms underlying biological processes during\\nmidlife play a key role in determining an individual s susceptibility', 'title': '2016 - Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging.pdf', 'version': 'v0', 'chunk_order': 70, 'document_id': '8cde78ac-cb0e-5983-86ee-91074b2fe1e3', 'extraction_id': '382122b9-6922-5d85-9e8c-acfa86aff085', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': '380ca35e-b42b-59b4-aef7-aaf2ba3bb59d', 'score': 0.679397661721847, 'metadata': {'text': 'span and have yielded insights into potential biological\\npathways and processes related to aging. Despite these\\nsuccesses, several problems are inherent in human\\nlongevity studies including potentially high degrees ofenvironmental heterogeneity, genetic diversity, and lack of\\nbirth matched controls, among others [ 8].\\nInbred mouse strains represent a powerful alternative for\\nidentifying genes underlying complex trait genes such as\\nlongevity [ 9]. Initial mapping approaches include quanti-', 'title': '2015 - A Chromosome 13 locus is associated with male-specific mortality in mice.pdf', 'version': 'v0', 'chunk_order': 8, 'document_id': 'ad8f2626-87fb-520e-8cef-ee9a9cc3ab0b', 'extraction_id': 'df0b4be9-3393-5642-a722-ccafffb60df8', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}, {'id': 'eea576fd-d766-5ae7-9e63-045869a3f8f7', 'score': 0.6727703809738159, 'metadata': {'text': 'Recently, the Atlas of Gene Expression in Mouse Aging Project\\n(AGEMAP) reported gene expression proles with age for 8932genes in 16 mouse tissues (Zahn et al ., 2007). We chose not to', 'title': '2009 - Meta-analysis of age-related gene expression profiles identifies.pdf', 'version': 'v0', 'chunk_order': 107, 'document_id': '5c2cf97f-a57a-5284-85a3-b8d9c5943113', 'extraction_id': '4d95f551-34bd-5e7a-8702-eb59de73a480', 'associatedQuery': 'How do I generate a linkage or association mapping study in mice to understand aging?'}}], 'kg_search_results': None}}\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "domain_expoert_aging_5\n", + "results --> {'completion': {'id': 'chatcmpl-ABLwzkPUEqxCEqW5L5wugbbowvYPv', 'choices': [{'finish_reason': 'stop', 'index': 0, 'message': {'content': \"Yes, there are specific genetic variations that can contribute to someone living longer. Research has shown that certain genes and their variations can influence longevity. For example, variations near the genes APOE, FOXO3A, and CHRNA3/5 have been robustly associated with lifespan [10]. These genetic variations can affect how our bodies age and how well we can avoid or delay age-related diseases.\\n\\nIn simpler terms, think of these genes as parts of a car. Just like how certain parts can make a car run more efficiently and last longer, these genetic variations can help our bodies function better and live longer. However, it's important to note that living a long life is usually a combination of both genetic factors and lifestyle choices, such as diet, exercise, and avoiding harmful habits.\", 'role': 'assistant'}}], 'created': 1727269349, 'model': 'gpt-4o-2024-05-13', 'object': 'chat.completion', 'system_fingerprint': 'fp_e375328146', 'usage': {'completion_tokens': 157, 'prompt_tokens': 1228, 'total_tokens': 1385}}, 'search_results': {'vector_search_results': [{'id': 'c2234f77-2268-57d0-a227-e931fc4802c1', 'score': 0.6878040619013285, 'metadata': {'text': 'GENOME-WIDE ASSOCIATION STUDY OF LONGEVITY 479\\nINCREASES in longevity of the general population world -\\nwide are an unprecedented phenomenon with significant \\nhealth and social impact. Although environmental factors \\nhave led to an increase in life span, there is ample evidence \\nthat genetic factors are involved in extreme longevity both \\nin humans (17) and in other organisms (8). The protective \\ngenetic factors that lead to longevity are likely to involve', 'title': '2010 - A Meta-analysis of Four Genome-Wide Association Studies.pdf', 'version': 'v0', 'chunk_order': 12, 'document_id': '8e452186-a71c-5b62-81b2-7681c87c8e1d', 'extraction_id': '8bc54e5b-f45f-54f9-9591-1e26dd80b50d', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': 'fb0af8f1-5b2a-5ba1-8a53-ee543a9267bf', 'score': 0.6867071390151978, 'metadata': {'text': 'that any genetic variant that contributes strongly to extremelongevity would also be rare. One possibility is that a specificmutation could alter the protein-coding region in a gene andconfer a significant increase in longevity. Such a mutation couldact in a dominant or recessive fashion, and might be shared by asignificant fraction of the supercentenarian genomes but not bycontrol genomes. We created a computational pipeline todetermine whether our supercentenarian genomes are enrichedfor such a variant', 'title': '2014 - Whole-Genome Sequencing of the World?s Oldest People.pdf', 'version': 'v0', 'chunk_order': 56, 'document_id': 'd2a5ec28-873a-5ff3-9cf4-dbec3b52dd21', 'extraction_id': 'c918522d-c0bf-5b7a-9ced-a69d485b2cb6', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '754929a6-af78-569a-969c-e750d174b952', 'score': 0.6830184459686279, 'metadata': {'text': 'ever, natural human and animal longevity is presumed to be acomplex trait (Finch & Tanzi, 1997). In humans, both candidategene and genome-wide genetic association approaches havebeen applied in an attempt to identify longevity loci. The fre-quency of genetic variants has been typically compared\\nbetween nonagenarian cases and young controls, revealing', 'title': '2011 - Genome-wide association study identifies a single major locus contributing to survival into old age the APOE locus revisited.pdf', 'version': 'v0', 'chunk_order': 13, 'document_id': '05208abc-5ac0-5d4d-b600-2caf59ce75b7', 'extraction_id': 'a4aa5d3a-81e8-582c-aee6-3ebdd329de86', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '4a6d2b9b-9496-5d90-a24a-43c643c4916b', 'score': 0.6809488534927368, 'metadata': {'text': 'genetic makeup of extreme longevity is based on a combination of common and rare variants, with common vari-ants that create the background to survive to relatively common old ages, and specific combinations of uncommon and rare variants that add an additional survival advantage to even older ages. Our analy-sis showed that LAVs discovered through a casecontrol study are not necessarily the variants that make someone live to extreme old age, and additional survival analysis is needed to characterize and', 'title': '2017 - Four Genome-Wide Association Studies Identify New.pdf', 'version': 'v0', 'chunk_order': 122, 'document_id': 'c10653f6-b3d7-5b92-9271-ab8fcc7905a7', 'extraction_id': 'b539194c-50bb-55e5-83b2-e779f63ed363', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '1f4437a7-cee1-5dc2-80e1-9924248857d0', 'score': 0.6716829538345337, 'metadata': {'text': 'genetic determination of human exceptional longevity, they arethe rst step toward the generation of a comprehensive referencepanel of exceptionally long-lived individuals. The data also provideinteresting insights into genetic backgrounds that are conduciveto exceptional longevity and allow us to test different models of\\nexceptional longevity.\\nwww.frontiersin.org January 2012 | Volume 2 | Article 90 | 1', 'title': '2012 - Whole genome sequences of a male and female supercentenarian, ages greater than 114 years.pdf', 'version': 'v0', 'chunk_order': 12, 'document_id': '408cdcd5-ab70-520a-b2c4-d9028b0a8d6f', 'extraction_id': '402ab5b5-e6fa-58fe-8f32-7c235be7a746', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '91010ff1-43a7-53f6-966d-601913e3b26b', 'score': 0.6682877142257873, 'metadata': {'text': 'tremely long lived individuals. Longevity has a genetic component, with an estimated heritability\\nof average life expectancy of approximately 25% (105, 106). Family studies of centenarians, thosewho live to 100 years or more, suggest that the relationship between genetics and longevity is\\nstronger in the oldest-old adults (107, 108), supporting the utility of long-lived individuals as a\\nmodel system for studying genetic variations that predispose people to longevity.', 'title': '2013 - Genome Instability and Aging.pdf', 'version': 'v0', 'chunk_order': 140, 'document_id': '71e08916-8cc8-5d96-8c06-4461b972b54d', 'extraction_id': 'f33756b1-7d64-5ab9-bcd6-717deaf05339', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '63ebd662-9aca-5b8a-b3e3-89860a45da42', 'score': 0.6676895220464765, 'metadata': {'text': 'because of genetic variation that becomes particularly important for sur-\\nvival at advanced age (Hjelmborg et al. , 2006). Epidemiological studies\\nhave revealed that long-lived individuals (LLI), that is, people surviving to\\nthe 95th percentile of the respective birth cohort-specic age distribu-\\ntions (Gudmundsson et al. , 2000), frequently show a favorable (healthy)\\ncourse of the aging process, with the absence or a delayed onset of age-', 'title': '2012 - Genome-wide miRNA signatures of human longevity.pdf', 'version': 'v0', 'chunk_order': 6, 'document_id': '18407659-c241-5f37-8ad2-ab59f6a7e288', 'extraction_id': 'e79b0811-a0f3-5f44-8004-89fe59aa8a3e', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '53a8e33f-da6f-5550-bf18-e45f2779f7a9', 'score': 0.6673998633146496, 'metadata': {'text': 'Studies of centenarians have provided strong evidence to sup-port the hypothesis that a genetic contribution to human excep-tional longevity is decisive, although only a small number ofgenetic variants with modest effects have been irrefutably linkedto this phenotype ( Schachter et al., 1994; Barzilai et al., 2003 ;\\nChristensen et al., 2006 ;Wheeler and Kim, 2011 ). The tech-\\nnology of next generation sequencing provides a tool to gen-erate data that may eventually provide an answer ( Metzker,\\n2009).', 'title': '2012 - Whole genome sequences of a male and female supercentenarian, ages greater than 114 years.pdf', 'version': 'v0', 'chunk_order': 10, 'document_id': '408cdcd5-ab70-520a-b2c4-d9028b0a8d6f', 'extraction_id': '402ab5b5-e6fa-58fe-8f32-7c235be7a746', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': '57227bee-d562-52c9-86dc-f9e2fcea1792', 'score': 0.6669017871080776, 'metadata': {'text': 'genetic contribution to human lifespan variation was estimated\\nat 2530% in twin studies (Gudmundsson et al. , 2000; Skytthe\\net al. , 2003; Hjelmborg et al. , 2006). The most prominent\\ngenetic inuence is observed in families in which the capacity toattain a long lifespan clusters (Perls et al. , 2000; Schoenmaker\\net al. , 2006). Exceptional longevity can be reached with a low\\ndegree of age-related disability (Christensen et al. , 2008; Terry\\net al. , 2008), raising the question whether protective mecha-', 'title': '2011 - Genome-wide association study identifies a single major locus contributing to survival into old age the APOE locus revisited.pdf', 'version': 'v0', 'chunk_order': 11, 'document_id': '05208abc-5ac0-5d4d-b600-2caf59ce75b7', 'extraction_id': 'a4aa5d3a-81e8-582c-aee6-3ebdd329de86', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}, {'id': 'b1b9f731-236c-5b4b-8cc6-fcf1e06d866a', 'score': 0.6654460430145264, 'metadata': {'text': 'age, usually de ned by a threshold, such as 90 years). Up to 25%\\nof the variability in human lifespan has been estimated to be\\ngenetic1, but genetic variation at only three loci (near APOE ,\\nFOXO3A and CHRNA3/5 )25have so far been demonstrated to\\nbe robustly associated with lifespan.\\nProspective genomic studies of lifespan have been hampered\\nby the fact that subject participation is often only recent,\\nallowing insuf cient follow-up time for a well-powered analysis of', 'title': '2017 - Genome-wide meta-analysis associates HLA.pdf', 'version': 'v0', 'chunk_order': 5, 'document_id': '3a565ba9-ee5b-5596-b870-ce8c055cb1f1', 'extraction_id': '9c6a9e93-5dc5-571d-b3c2-b600ed95e102', 'associatedQuery': 'is there a specific genetic variation that can cause someone to live longer? please make your answer accessible to a non-expert'}}], 'kg_search_results': None}}\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "domain_expoert_aging_6\n" ] } ], "source": [ - "def iterate_json(obj, thedict):\n", - " if isinstance(obj, dict):\n", - " for key, val in obj.items():\n", - " if (key == \"text\"):\n", - " thedict[\"contexts\"].append(val.replace(\"\\n\", \" \").strip())\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"associatedQuery\"):\n", - " #thedict[\"answer\"] = val#.replace(\"\\n\", \" \").strip()\n", - " thedict[\"question\"] = val#.replace(\"\\n\", \" \").strip()\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"id\"):\n", - " thedict[\"id\"].append(val.replace(\"\\n\", \" \").strip())\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"title\"):\n", - " thedict[\"titles\"].append(val.replace(\"\\n\", \" \").strip())\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"document_id\"):\n", - " thedict[\"document_id\"].append(val.replace(\"\\n\", \" \").strip())\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"content\"):\n", - " thedict[\"answer\"] = val.replace(\"\\n\", \" \").strip()\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " elif (key == \"extraction_id\"):\n", - " thedict[\"extraction_id\"].append(val.replace(\"\\n\", \" \").strip())\n", - " print((\"\", \"Key -> {0}\\tValue -> {1}\".format(key,val)) [verbose])\n", - " else:\n", - " if (len(obj.items()) == 1 ):\n", - " print(key, \" --> \", val)\n", - " iterate_json(val, thedict)\n", - " elif isinstance(obj, list):\n", - " for item in obj:\n", - " iterate_json(item, thedict)\n", - "\n", "# this should be a json file with a list of input files and an output file\n", "with open(read_file, \"r\") as r_file:\n", " result_file = json.load(r_file)\n", "\n", "ragas_output = {\n", - " \"titles\": [],\n", + " \"titles\": [],\n", " \"extraction_id\": [],\n", - " \"document_id\": [],\n", - " \"id\": [],\n", - " \"contexts\": [],\n", - " \"answer\": \"\",\n", - " \"question\": \"\"}\n", - "vector_search_results = result_file[\"vector_search_results\"]\n", - "choices = result_file[\"choices\"]\n", - "iterate_json(vector_search_results, ragas_output)\n", - "iterate_json(choices, ragas_output)\n" + " \"document_id\": [],\n", + " \"id\": [],\n", + " \"contexts\": [],\n", + " \"answer\": \"\",\n", + " \"question\": \"\"}\n", + "#extract_response(result_file, values_key, ragas_output)\n", + "print('There are {0} keys in the result file'.format(result_file.keys()))\n", + "for key in result_file.keys():\n", + " eval_dataset_dict = get_ragas_out_dict()\n", + " extract_response(result_file[key], values_key, eval_dataset_dict)\n", + " DocOps.writeDatasetFile(eval_dataset_dict, '../data/dataset/domain_expert_aging_{0}'.format(key))\n", + "\n" ] }, { @@ -159,7 +497,7 @@ }, { "cell_type": "code", - "execution_count": 119, + "execution_count": 36, "metadata": {}, "outputs": [ { @@ -167,68 +505,13 @@ "output_type": "stream", "text": [ "{\n", - " \"titles\": [\n", - " \"2011 - Annotating individual human genomes.pdf\",\n", - " \"2011 - Annotating individual human genomes.pdf\",\n", - " \"2011 - Annotating individual human genomes.pdf\",\n", - " \"2012 - Systems Biology Approaches to Nutrition.pdf\",\n", - " \"2006 - \\u03b22-adrenergic receptor and UCP3 variants modulate the relationship between age and type 2 diabetes mellitus.pdf\",\n", - " \"2001 - Demography in the age of genomics.pdf\",\n", - " \"2012 - Systems Biology Approaches to Nutrition.pdf\",\n", - " \"2004 - A genome scan for diabetic nephropathy in African Americans.pdf\",\n", - " \"2011 - Annotating individual human genomes.pdf\",\n", - " \"2012 - Systems Biology Approaches to Nutrition.pdf\"\n", - " ],\n", - " \"extraction_id\": [\n", - " \"80d78615-8424-5478-a01b-73e220bc0345\",\n", - " \"80d78615-8424-5478-a01b-73e220bc0345\",\n", - " \"80d78615-8424-5478-a01b-73e220bc0345\",\n", - " \"eb3de845-98db-505c-bb7f-c0f3259875fc\",\n", - " \"acf69ed8-c7b0-5d9f-8005-de020c9cf699\",\n", - " \"5f24a851-1de6-5b6e-8230-2da08806b01a\",\n", - " \"eb3de845-98db-505c-bb7f-c0f3259875fc\",\n", - " \"01ec7832-8a80-5f5e-aa26-3648f572c4a1\",\n", - " \"c17c74fa-12a3-5072-bb48-c179055db14d\",\n", - " \"eb3de845-98db-505c-bb7f-c0f3259875fc\"\n", - " ],\n", - " \"document_id\": [\n", - " \"f7b5d738-3f0b-5074-9c21-f6b443b4e07f\",\n", - " \"f7b5d738-3f0b-5074-9c21-f6b443b4e07f\",\n", - " \"f7b5d738-3f0b-5074-9c21-f6b443b4e07f\",\n", - " \"6955478b-950d-5d29-b24c-3a5ca656f3ae\",\n", - " \"0ea34c04-5d09-5a32-89a7-c3add179927a\",\n", - " \"0f07fa43-feb6-5656-b7e7-b8faa86f5623\",\n", - " \"6955478b-950d-5d29-b24c-3a5ca656f3ae\",\n", - " \"5798fb6b-b3e6-57c4-9823-5428853dbfa1\",\n", - " \"f7b5d738-3f0b-5074-9c21-f6b443b4e07f\",\n", - " \"6955478b-950d-5d29-b24c-3a5ca656f3ae\"\n", - " ],\n", - " \"id\": [\n", - " \"7656b48b-d191-516e-9753-d34efedd4812\",\n", - " \"d1af5c82-d226-5980-b5d9-90d7558d1880\",\n", - " \"bb2a67ec-135b-5d55-b33d-74b1dc085685\",\n", - " \"11fc663d2-2833-51e7-ae6a-55b007a6e27c\",\n", - " \"bb55a705-7399-550e-8285-07c33654b909\",\n", - " \"9bff43c0-fd12-572e-9996-24957edd17d2\",\n", - " \"2df84ccc-0d32-582e-bda6-9cd46bee5378\",\n", - " \"ff30f187-d5c3-5d01-8026-0588a77e9f44\",\n", - " \"57dc1ee5-4252-52c3-92cb-e2ac36cdc4d6\",\n", - " \"ff801099-e737-57b1-91af-a4cea20adb87\"\n", - " ],\n", - " \"contexts\": [\n", - " \"gene interaction and high predictive value, PLoS One 3 (5) (2008) e2031,doi:10.1371/journal.pone.0002031 . [107] M. van Hoek, A. Dehghan, J.C. Witteman, C.M. van Duijn, A.G. Uitterlinden, B.A. Oostra, A. Hofman, E.J. Sijbrands, A.C. Janssens, Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study, Diabetes 57 (11) (Nov 2008) 3122 3128. [108] Q. Lu, Y. Song, X. Wang, S. Won, Y. Cui, R.C. Elston, The effect of multiple genetic\",\n", - " \"variants in predicting the risk of type 2 diabetes, BMC Proc 3 (Suppl 7) (Dec 15 2009) S49. [109] K. Miyake, W. Yang, K. Hara, K. Yasuda, Y. Horikawa, H. Osawa, H. Furuta, et al., Construction of a prediction model for type 2 diabetes mellitus in the Japanese population based on 11 genes with strong evidence of the association, J. Hum. Genet. 54 (4) (Apr 2009) 236 241 [Epub 2009 Feb 27]. [110] P.J. Talmud, A.D. Hingorani, J.A. Cooper, M.G. Marmot, E.J. Brunner, M. Kumari, M.\",\n", - " \"type 2 diabetes risk, Diabetes 57 (11) (Nov 2008) 3129 3135. [103] Q. Lu, R.C. Elston, Using the optimal receiver operating characteristic curve to design a predictive genetic test, exempli ed with type 2 diabetes, Am. J. Hum. Genet. 82 (3) (Mar 2008) 641 651. [104] V. Lyssenko, A. Jonsson, P. Almgren, N. Pulizzi, B. Isomaa, T. Tuomi, G. Berglund, D. Altshuler, P. Nilsson, L. Groop, Clinical risk factors, DNA variants, and the development of type 2 diabetes, N. Engl. J. Med. 359 (21) (Nov 20 2008)\",\n", - " \"insulin resistance, hypertension, and dyslipidemia (Obesity Education Initiative Expert Panel, 1998 ). Insulin resist-ance increases with age, and the incidence of diabetes rises sharply in the elderly (American Diabetes Association, 2010a ). In a few patients, genetic mutations appear to be associ- ated with T2D (Roche et al. , 2005 ; American Diabetes Association, 2010a ). For example, recent work using the DPP data has led to the identi cation of 27 single nucle-\",\n", - " \"19. Permutt MA, Wasson J, Cox N: Genetic epidemiology of diabe- tes. J Clin Invest 2005, 115:1431-1439. 20. Barroso I: Genetics of Type 2 diabetes. Diabet Med 2005, 22:517-535. 21. Parikh H, Groop L: Candidate genes for type 2 diabetes. Rev Endocr Metab Disord 2004, 5:151-176. 22. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN: Meta- analysis of genetic association studies supports a contribu- tion of common variants to su sceptibility to common dis- ease. Nat Genet 2003, 33:177-182.\",\n", - " \"insulin-dependent diabetes and schizophrenia, twin studies have demon-strated the existence of a significant genetic component (Kyvik et al., 1995;Plomin et al., 1994). Genetic factors also influence cardiovascular diseaseswhich occur in early or midlife, while for cardiovascular diseases occur-ring late in life there is little evidence of a genetic effect (Marenberg et al.,1994). Dementia has a very strong genetic component, not only withregard to early-onset monogenic types but also to late-onset\",\n", - " \"Three categories of increased risk of developing diabetes are currently recognized by the ADA: an FPG between 5.6 and 6.9 mmol/L (100 and 125 mg/dL), de ned as having impaired fasting glucose (IFG); a 2 - h OGTT between 7.8 and 11 mmol/L (140 and 199 mg/dL), de ned as having impaired glucose tolerance (IGT); an A1C between 5.7 and 6.4% with values between 6.0 and 6.4 considered very high risk (American Diabetes Association, 2010a ). It is estimated that approximately one - fourth of indi-\",\n", - " \"20 90 D20S451 0.006 10.7 5.4 (34) 8.42 5.4 (61) 0.30 (long duration) Interaction with age at diagnosis of diabetes 19 1 D1S1665 0.004 37.4 8.1 (66) 41.2 8.3 (81) 0.23 (early onset) 2 159 D2S1399/D2S1353 0.023 40.8 8.2 (53) 38.8 8.5 (94) 0.16 (late onset) 3 135 D3S2460 0.036 37.7 8.6 (66) 41.0 8.0 (81) 0.16 (early onset) 4 146 D4S1625 0.005 37.9 7.4 (52) 40.4 8.9 (95) 0.23 (early onset) 65 5 D6S2427 0.024 38.0 7.8 (70) 40.9 8.8 (77) 0.18 (early onset)\",\n", - " \"prevention, even though there are great concerns about how such information will be perceived and utilized [68]. Recent studies in diabetes and cardiovascular disease suggest that the addition of previously associated genetic risk loci in clinical risk models of those diseases increases both discriminative and predictive accuracy, albeit only marginally. Typically, the strongest predictors of disease onset are known clinical risk factors such as body mass index, age, or\",\n", - " \"and sex, weight for height greater than the 85th percentile, or weight greater than 120% of ideal for height) who also have any two of the following risk factors: family history of T2D ( rst - or second - degree relative), maternal history of diabetes or GDM during child s gestation, member of high - risk race/ethnicity group (Native American, African -(40 in) in men is considered an indicator of increased\"\n", - " ],\n", - " \"answer\": \"The factors that help predict early onset of diabetes include: 1. **Genetic Factors**: Specific genetic mutations and polymorphisms have been associated with an increased risk of developing type 2 diabetes (T2D) [1], [2], [4], [5], [6], [8]. 2. **Clinical Risk Factors**: Known clinical risk factors such as body mass index (BMI), age, and sex are strong predictors of disease onset [9]. 3. **Family History**: A family history of T2D, particularly in first- or second-degree relatives, is a significant risk factor [10]. 4. **Maternal History**: A maternal history of diabetes or gestational diabetes mellitus (GDM) during the childs gestation increases the risk [10]. 5. **Ethnicity**: Being a member of a high-risk race/ethnicity group, such as Native American or African American, is associated with a higher risk [10]. 6. **Impaired Glucose Levels**: Impaired fasting glucose (IFG), impaired glucose tolerance (IGT), and elevated A1C levels are indicators of increased risk [7]. 7. **Insulin Resistance and Related Conditions**: Conditions such as insulin resistance, hypertension, and dyslipidemia are linked to a higher risk of developing diabetes [4]. These factors collectively contribute to the prediction of early onset diabetes.\",\n", - " \"question\": \"List any factors that help predict early onset of diabetes.\"\n", + " \"titles\": [],\n", + " \"extraction_id\": [],\n", + " \"document_id\": [],\n", + " \"id\": [],\n", + " \"contexts\": [],\n", + " \"answer\": \"\",\n", + " \"question\": \"\"\n", "}\n" ] } |