Docker image built to run code, all evals run using R2RHEADmaster

1 files changed, 65 insertions, 0 deletions

diff --git a/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_12 b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_12
new file mode 100644
index 0000000..73a4c9b
--- /dev/null
+++ b/gnqa/paper2_eval/data/dataset/human/intermediate_files/human_cs_aging_12
@@ -0,0 +1,65 @@
+{
+  "titles": [
+    "2012 - Genome-Environment Interactions That Modulate.pdf",
+    "2009 - The Human Ageing Genomic Resources online.pdf",
+    "2010 - Do different neurons age differently Direct genome-wide analysis of aging in single identified cholinergic neurons.pdf",
+    "2011 - A genome-wide association study of aging.pdf",
+    "2009 - The Human Ageing Genomic Resources online.pdf",
+    "2018 - Biological Processes Modulating Longevity across Primates.pdf",
+    "2009 - The Human Ageing Genomic Resources online.pdf",
+    "2009 - The Human Ageing Genomic Resources online.pdf",
+    "2010 - Genetics and genomics of human ageing.pdf",
+    "2011 - Genetics and genomics of human ageing.pdf"
+  ],
+  "extraction_id": [
+    "d59d7882-333d-5576-86ab-3cfa6354b946",
+    "52c67b46-63f2-54ae-a78e-e9d54a55f6e4",
+    "81c68113-aa96-5af3-b4fc-5898fa20e379",
+    "a5be18f8-c263-5635-87d7-57c5addd65e5",
+    "52c67b46-63f2-54ae-a78e-e9d54a55f6e4",
+    "c07d6709-8dbe-5437-b7df-0849b92c0ea0",
+    "52c67b46-63f2-54ae-a78e-e9d54a55f6e4",
+    "52c67b46-63f2-54ae-a78e-e9d54a55f6e4",
+    "59227f74-f1c7-58ad-a886-aa9e3799a132",
+    "07a34581-749c-5556-bdea-806b2c9c7915"
+  ],
+  "document_id": [
+    "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec",
+    "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529",
+    "153b070f-0291-5ed4-ad33-edea5e3fa8f7",
+    "8e9c1150-1047-54a2-bf85-1cc5000a6811",
+    "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529",
+    "930103c1-e98e-524c-aa68-233a45dc6726",
+    "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529",
+    "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529",
+    "633f3149-e966-53ef-aa7d-b759398ed541",
+    "08eee102-d627-5f1b-84c7-603c38981adf"
+  ],
+  "id": [
+    "chatcmpl-ADZWOuZDmIcGuvC8wjb6oX7vSBFDg",
+    "786d2756-4c4d-5ac0-8d3d-63f914d51664",
+    "a21de3e8-ed2c-5c06-a351-ccb8f92f4e21",
+    "6f04401a-b938-5a60-8b69-d37f9086748c",
+    "06e319e1-b054-5f33-9b40-ee892f507736",
+    "9defe0af-80a1-56da-90df-551fd55baa13",
+    "f2fbfb29-0a51-5f94-8b67-d47ab4de68bd",
+    "8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb",
+    "650300e1-898c-56e2-9358-0bb6625b0073",
+    "df45a752-e866-54bb-ab49-daff9a702eef",
+    "fd6cfc2c-76b1-5620-a68c-fb37db9b6f78"
+  ],
+  "contexts": [
+    "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-",
+    "GenAge features a data set of genes that may regulate agingin humans or that at least appear to be considerably associated with the human aging phenotype. This data set includes orthologues  derived from established databases, mainly In-Paranoid (OBrien   et     al  ., 2005) but also HomoloGene (http://",
+    "OTHER AGING RELATED GENES",
+    "processes in human longevity and aging. Ten of the 22 suggestive associations identied in our analyses are in ornear genes that are highly expressed in the brain (HECW2[Rotin and Kumar, 2009], HIP1 [Blanpied et al., 2003], BIN2, GRIA1), were previously related to the regulation of neuronal excitability and plasticity (KCNQ4 [Van Eyken et al., 2006], LMO4 [Joshi et al., 2009; Leuba et al., 2004],",
+    "genes analyzed for their possible association with human lon-gevity (http://genomics.senescence.info/genes/longevity.html).All longevity association studies in humans we could find by thetime of the latest update were added to this list. These includestudies reporting negative results, which we see as essentialsince many genes display population-specific associations withlongevity. Fig. 1 From the main page of the Human Ageing",
+    "Pleiotropies and Aging-Related Genesets To study genes that have been previously related to aging, a list of curated human genes associated with aging in different model systems was obtained from the GenAge data set ( de Magalh ~aes et al. 2005 ). We used gene ontology (GO) anno-",
+    "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",
+    "shown that genes associated with aging and/or longevity inmodel organisms are evolutionary conserved in terms of havingmore homologues than predicted by chance (Budovsky   et     al  .,2007, 2008) and exhibiting slower molecular evolution rates (de Magalhes & Church, 2007). Therefore, it is now clear that atleast some genes identified in model organisms may be relevantto human aging. To allow researchers to focus specifically on human aging,",
+    "aging in human muscle reveals a common aging signa-ture. PLoS Genet. 2, e115. ( doi:10.1371/journal.pgen. 0020115 ) 64 Lener, T ., Moll, P . R., Rinnerthaler, M., Bauer, J., Aberger, F. & Richter, K. 2006 Expression proling ofaging in the human skin. Exp. Gerontol. 41, 387397. (doi:10.1016/j.exger.2006.01.012 ) 65 Kim, S. K. 2008 Genome-wide views of aging gene net- works . Molecular Biology of Aging Monograph 9. Cold Spring Harbor, CT: Cold Spring Harbor LaboratoryPress.",
+    "aging in human muscle reveals a common aging signa-ture. PLoS Genet. 2, e115. ( doi:10.1371/journal.pgen. 0020115 ) 64 Lener, T ., Moll, P . R., Rinnerthaler, M., Bauer, J., Aberger, F. & Richter, K. 2006 Expression proling ofaging in the human skin. Exp. Gerontol. 41, 387397. (doi:10.1016/j.exger.2006.01.012 ) 65 Kim, S. K. 2008 Genome-wide views of aging gene net- works . Molecular Biology of Aging Monograph 9. Cold Spring Harbor, CT: Cold Spring Harbor LaboratoryPress."
+  ],
+  "answer": "Several genes have been associated with aging in humans according to the provided context:  1. **GenAge Data Set**: This data set includes genes that may regulate aging in humans or are considerably associated with the human aging phenotype [2]. 2. **HECW2, HIP1, BIN2, GRIA1, KCNQ4, LMO4**: These genes are highly expressed in the brain and have been previously related to the regulation of neuronal excitability and plasticity [4]. 3. **Werners Syndrome Gene**: Mutations in this gene result in segmental progeroid syndromes, which are critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway [7].  These references indicate that there are multiple genes associated with aging in humans, with some being highly expressed in specific tissues like the brain and others being involved in critical aging-related pathways.",
+  "question": "Which genes are associated with aging in human"
+}
\ No newline at end of file