bonito_variation

README.md

@@ -4,22 +4,30 @@ configs:
   data_files:
   - path: unannotated_ncbi_summary/*.json
     split: train
-- config_name: ncbi_qa
+- config_name: question_answering_without_choices
   data_files:
   - path: ncbi_qa/*.json
     split: train
-- config_name: ncbi_nli
+- config_name: natural_language_inference
   data_files:
   - path: ncbi_nli/*.json
     split: train
-- config_name: ncbi_cr
+- config_name: coreference_resolution
   data_files:
   - path: ncbi_cr/*.json
     split: train
-- config_name: ncbi_mcqa
+- config_name: multiple_choice_question_answering
   data_files:
   - path: ncbi_mcqa/*.json
     split: train
+- config_name: extractive_question_answering
+  data_files:
+  - path: ncbi_exqa/*.json
+    split: train
+- config_name: textual_entailment
+  data_files:
+  - path: ncbi_te/*.json
+    split: train
 task_categories:
 - text2text-generation
 language:

ncbi_exqa/ncbi_summary_exqa.json

@@ -0,0 +1,10 @@
+{"input": "A1BG, Official Symbol A1BGprovided by HGNC Official Full Name alpha-1-B glycoproteinprovided by HGNC Primary source HGNC:HGNC:5 See related Ensembl:ENSG00000121410 MIM:138670; AllianceGenome:HGNC:5 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A1B; ABG; GAB; HYST2477 Summary The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. [provided by RefSeq, Jul 2008] Orthologs mouse all\n\nQ: What is the official symbol for A1BG?\n\nReferring to the passage above, the correct answer to the given question is", "output": "A1BG"}
+{"input": "A1BG-AS1, Official Symbol A1BG-AS1provided by HGNC Official Full Name A1BG antisense RNA 1provided by HGNC Primary source HGNC:HGNC:37133 See related Ensembl:ENSG00000268895 AllianceGenome:HGNC:37133 Gene type ncRNA RefSeq status PREDICTED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A1BGAS; A1BG-AS; NCRNA00181 Expression Biased expression in liver (RPKM 106.5) and spleen (RPKM 1.9) See more\n\nQ: What is the full name of the A1BG-AS1?\n\nA:", "output": "A1BG antisense RNA 1"}
+{"input": "I have a new situation: David wants to go into more detail about a certain protein that he found interesting. He notes this protein as protein A. David's colleague, Frank, helps David by providing him with another protein that is similar to protein A. Frank notes this protein as protein B. David and Frank are planning to do more research on these proteins in the future.\n\nBut I can use this background: A1CF, Official Symbol A1CFprovided by HGNC Official Full Name APOBEC1 complementation factorprovided by HGNC Primary source HGNC:HGNC:24086 See related Ensembl:ENSG00000148584 MIM:618199; AllianceGenome:HGNC:24086 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as ACF; ASP; ACF64; ACF65; APOBEC1CF Summary Mammalian apolipoprotein B mRNA undergoes site-specific C to U deamination, which is mediated by a multi-component enzyme complex containing a minimal core composed of APOBEC-1 and a complementation factor encoded by this gene. The gene product has three non-identical RNA recognition motifs and belongs to the hnRNP R family of RNA-binding proteins. It has been proposed that this complementation factor functions as an RNA-binding subunit and docks APOBEC-1 to deaminate the upstream cytidine. Studies suggest that the protein may also be involved in other RNA editing or RNA processing events. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Nov 2010] Expression Biased expression in liver (RPKM 31.2), small intestine (RPKM 8.6) and 4 other tissues See more Orthologs mouse all\n\nWhat is an answer for this question: Which protein is involved in other RNA editing or RNA processing events?", "output": "protein A"}
+{"input": "A2M, Official Symbol A2Mprovided by HGNC Official Full Name alpha-2-macroglobulinprovided by HGNC Primary source HGNC:HGNC:7 See related Ensembl:ENSG00000175899 MIM:103950; AllianceGenome:HGNC:7 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A2MD; CPAMD5; FWP007; S863-7 Summary The protein encoded by this gene is a protease inhibitor and cytokine transporter. It uses a bait-and-trap mechanism to inhibit a broad spectrum of proteases, including trypsin, thrombin and collagenase. It can also inhibit inflammatory cytokines, and it thus disrupts inflammatory cascades. Mutations in this gene are a cause of alpha-2-macroglobulin deficiency. This gene is implicated in Alzheimer's disease (AD) due to its ability to mediate the clearance and degradation of A-beta, the major component of beta-amyloid deposits. A related pseudogene, which is also located on the p arm of chromosome 12, has been identified. [provided by RefSeq, Nov 2016] Expression Broad expression in lung (RPKM 732.0), urinary bladder (RPKM 374.7) and 21 other tissues See more Orthologs all\n\nQ: What is the full name of the protein encoded by the A2M gene?\n\nA:", "output": "alpha-2-macroglobulin"}
+{"input": "A2M-AS1, Official Symbol A2M-AS1provided by HGNC Official Full Name A2M antisense RNA 1provided by HGNC Primary source HGNC:HGNC:27057 See related Ensembl:ENSG00000245105 AllianceGenome:HGNC:27057 Gene type ncRNA RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Expression Broad expression in lung (RPKM 20.8), liver (RPKM 9.6) and 21 other tissues See more\n\nQ: What is the official symbol of A2M-AS1?\n\nReferring to the passage above, the correct answer to the given question is", "output": "A2M-AS1"}
+{"input": "A2ML1, Official Symbol A2ML1provided by HGNC Official Full Name alpha-2-macroglobulin like 1provided by HGNC Primary source HGNC:HGNC:23336 See related Ensembl:ENSG00000166535 MIM:610627; AllianceGenome:HGNC:23336 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as OMS; p170; CPAMD9 Summary This gene encodes a member of the alpha-macroglobulin superfamily. The encoded protein is thought to be an N-glycosylated monomeric protein that acts as an inhibitor of several proteases. It has been shown to form covalent interactions with proteases, and has been reported as the p170 antigen recognized by autoantibodies in the autoimmune disease paraneoplastic pemphigus (PNP; PMID:20805888). Mutations in these gene have also been associated with some cases of Noonan syndrome (NS; PMID:24939586) as well as some cases of otitis media (PMID:26121085). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015] Expression Restricted expression toward esophagus (RPKM 190.0) See more Orthologs all\n\nQ: What is the official symbol for A2ML1?\n\nReferring to the passage above, the correct answer to the given question is", "output": "A2ML1"}
+{"input": "A2ML1-AS1, Official Symbol A2ML1-AS1provided by HGNC Official Full Name A2ML1 antisense RNA 1provided by HGNC Primary source HGNC:HGNC:41022 See related AllianceGenome:HGNC:41022 Gene type ncRNA RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Annotation information not in current annotation release\n\nQ: What is the primary source of A2ML1-AS1?\n\nA:", "output": "HGNC"}
+{"input": "A2MP1, Official Symbol A2MP1provided by HGNC Official Full Name alpha-2-macroglobulin pseudogene 1provided by HGNC Primary source HGNC:HGNC:8 See related Ensembl:ENSG00000291190 AllianceGenome:HGNC:8 Gene type pseudo RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A2MP Expression Biased expression in adrenal (RPKM 1.1), spleen (RPKM 0.5) and 11 other tissues See more\n\nQ: What is the official symbol for A2MP1?\n\nA:", "output": "A2MP1"}
+{"input": "I have a new situation: David is a molecular biologist. He is studying the differences between two proteins, protein A and protein B. Protein A is from Homo sapiens, but protein B is from mouse. He needs to figure out how they differ in terms of functionality and structure.\n\nBut I can use this background: A3GALT2, Official Symbol A3GALT2provided by HGNC Official Full Name alpha 1,3-galactosyltransferase 2provided by HGNC Primary source HGNC:HGNC:30005 See related Ensembl:ENSG00000184389 MIM:619850; AllianceGenome:HGNC:30005 Gene type protein coding RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as IGB3S; IGBS3S; A3GALT2P Summary Predicted to enable N-acetyllactosaminide 3-alpha-galactosyltransferase activity and alpha-1,3-galactosyltransferase activity. Predicted to be involved in lipid glycosylation. Predicted to act upstream of or within glycosphingolipid biosynthetic process. Predicted to be located in Golgi cisterna membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and vesicle. [provided by Alliance of Genome Resources, Apr 2022] Expression Low expression observed in reference dataset See more Orthologs mouse all\n\nWhat is an answer for this question: Which protein is more likely to be active in Golgi apparatus, protein A or protein B?", "output": "protein A"}
+{"input": "I have a new situation: John is a biologist. He had some samples of blood from various individuals. He grouped them into two groups, group P and group Q. He noticed that group P had P(k) antigen, but group Q didn't have P(k) antigen. He needed to know the reason for this difference.\n\nBut I can use this background: A4GALT, Official Symbol A4GALTprovided by HGNC Official Full Name alpha 1,4-galactosyltransferase (P blood group)provided by HGNC Primary source HGNC:HGNC:18149 See related Ensembl:ENSG00000128274 MIM:607922; AllianceGenome:HGNC:18149 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as P1; PK; Gb3S; P(k); P1PK; A14GALT; A4GALT1 Summary The protein encoded by this gene catalyzes the transfer of galactose to lactosylceramide to form globotriaosylceramide, which has been identified as the P(k) antigen of the P blood group system. This protein, a type II membrane protein found in the Golgi, is also required for the synthesis of the bacterial verotoxins receptor. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015] Expression Ubiquitous expression in kidney (RPKM 6.5), fat (RPKM 5.5) and 22 other tissues See more Orthologs mouse all\n\nWhat is an answer for this question: Which group would have Ubiquitous expression in kidney, group P or group Q?", "output": "group P"}

ncbi_te/ncbi_summary_te.json

@@ -0,0 +1,10 @@
+{"input": "A1BG, Official Symbol A1BGprovided by HGNC Official Full Name alpha-1-B glycoproteinprovided by HGNC Primary source HGNC:HGNC:5 See related Ensembl:ENSG00000121410 MIM:138670; AllianceGenome:HGNC:5 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A1B; ABG; GAB; HYST2477 Summary The protein encoded by this gene is a plasma glycoprotein of unknown function. The protein shows sequence similarity to the variable regions of some immunoglobulin supergene family member proteins. [provided by RefSeq, Jul 2008] Orthologs mouse all\nQuestion: A1BG is a protein. True or False?", "output": "True"}
+{"input": "Given that A1BG-AS1, Official Symbol A1BG-AS1provided by HGNC Official Full Name A1BG antisense RNA 1provided by HGNC Primary source HGNC:HGNC:37133 See related Ensembl:ENSG00000268895 AllianceGenome:HGNC:37133 Gene type ncRNA RefSeq status PREDICTED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A1BGAS; A1BG-AS; NCRNA00181 Expression Biased expression in liver (RPKM 106.5) and spleen (RPKM 1.9) See more Therefore, it must be true that \"A1BG-AS1 is the official symbol of HGNC.\"? Yes or no?", "output": "Yes"}
+{"input": "Given that A1CF, Official Symbol A1CFprovided by HGNC Official Full Name APOBEC1 complementation factorprovided by HGNC Primary source HGNC:HGNC:24086 See related Ensembl:ENSG00000148584 MIM:618199; AllianceGenome:HGNC:24086 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as ACF; ASP; ACF64; ACF65; APOBEC1CF Summary Mammalian apolipoprotein B mRNA undergoes site-specific C to U deamination, which is mediated by a multi-component enzyme complex containing a minimal core composed of APOBEC-1 and a complementation factor encoded by this gene. The gene product has three non-identical RNA recognition motifs and belongs to the hnRNP R family of RNA-binding proteins. It has been proposed that this complementation factor functions as an RNA-binding subunit and docks APOBEC-1 to deaminate the upstream cytidine. Studies suggest that the protein may also be involved in other RNA editing or RNA processing events. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Nov 2010] Expression Biased expression in liver (RPKM 31.2), small intestine (RPKM 8.6) and 4 other tissues See more Orthologs mouse all Therefore, it must be true that \"A1CF is a protein coding gene.\"? Yes or no?", "output": "Yes"}
+{"input": "A2M, Official Symbol A2Mprovided by HGNC Official Full Name alpha-2-macroglobulinprovided by HGNC Primary source HGNC:HGNC:7 See related Ensembl:ENSG00000175899 MIM:103950; AllianceGenome:HGNC:7 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A2MD; CPAMD5; FWP007; S863-7 Summary The protein encoded by this gene is a protease inhibitor and cytokine transporter. It uses a bait-and-trap mechanism to inhibit a broad spectrum of proteases, including trypsin, thrombin and collagenase. It can also inhibit inflammatory cytokines, and it thus disrupts inflammatory cascades. Mutations in this gene are a cause of alpha-2-macroglobulin deficiency. This gene is implicated in Alzheimer's disease (AD) due to its ability to mediate the clearance and degradation of A-beta, the major component of beta-amyloid deposits. A related pseudogene, which is also located on the p arm of chromosome 12, has been identified. [provided by RefSeq, Nov 2016] Expression Broad expression in lung (RPKM 732.0), urinary bladder (RPKM 374.7) and 21 other tissues See more Orthologs all Are we justified in saying that \"A2M is a protease inhibitor.\"? Yes or no?", "output": "Yes"}
+{"input": "A2M-AS1, Official Symbol A2M-AS1provided by HGNC Official Full Name A2M antisense RNA 1provided by HGNC Primary source HGNC:HGNC:27057 See related Ensembl:ENSG00000245105 AllianceGenome:HGNC:27057 Gene type ncRNA RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Expression Broad expression in lung (RPKM 20.8), liver (RPKM 9.6) and 21 other tissues See more \n\nQuestion: Does this imply that \"A2M-AS1 is a ncRNA.\"? Yes or no?", "output": "Yes"}
+{"input": "A2ML1, Official Symbol A2ML1provided by HGNC Official Full Name alpha-2-macroglobulin like 1provided by HGNC Primary source HGNC:HGNC:23336 See related Ensembl:ENSG00000166535 MIM:610627; AllianceGenome:HGNC:23336 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as OMS; p170; CPAMD9 Summary This gene encodes a member of the alpha-macroglobulin superfamily. The encoded protein is thought to be an N-glycosylated monomeric protein that acts as an inhibitor of several proteases. It has been shown to form covalent interactions with proteases, and has been reported as the p170 antigen recognized by autoantibodies in the autoimmune disease paraneoplastic pemphigus (PNP; PMID:20805888). Mutations in these gene have also been associated with some cases of Noonan syndrome (NS; PMID:24939586) as well as some cases of otitis media (PMID:26121085). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015] Expression Restricted expression toward esophagus (RPKM 190.0) See more Orthologs all Based on the previous passage, is it true that \"The OMS gene is a member of the alpha-macroglobulin superfamily.\"? Yes or no?", "output": "Yes"}
+{"input": "Given that A2ML1-AS1, Official Symbol A2ML1-AS1provided by HGNC Official Full Name A2ML1 antisense RNA 1provided by HGNC Primary source HGNC:HGNC:41022 See related AllianceGenome:HGNC:41022 Gene type ncRNA RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Annotation information not in current annotation release Does it follow that A2ML1-AS1 is a gene. Yes or no?", "output": "Yes"}
+{"input": "A2MP1, Official Symbol A2MP1provided by HGNC Official Full Name alpha-2-macroglobulin pseudogene 1provided by HGNC Primary source HGNC:HGNC:8 See related Ensembl:ENSG00000291190 AllianceGenome:HGNC:8 Gene type pseudo RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as A2MP Expression Biased expression in adrenal (RPKM 1.1), spleen (RPKM 0.5) and 11 other tissues See more Are we justified in saying that \"HGNC is the official symbol of A2MP1.\"? Yes or no?", "output": "Yes"}
+{"input": "A3GALT2, Official Symbol A3GALT2provided by HGNC Official Full Name alpha 1,3-galactosyltransferase 2provided by HGNC Primary source HGNC:HGNC:30005 See related Ensembl:ENSG00000184389 MIM:619850; AllianceGenome:HGNC:30005 Gene type protein coding RefSeq status VALIDATED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as IGB3S; IGBS3S; A3GALT2P Summary Predicted to enable N-acetyllactosaminide 3-alpha-galactosyltransferase activity and alpha-1,3-galactosyltransferase activity. Predicted to be involved in lipid glycosylation. Predicted to act upstream of or within glycosphingolipid biosynthetic process. Predicted to be located in Golgi cisterna membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus and vesicle. [provided by Alliance of Genome Resources, Apr 2022] Expression Low expression observed in reference dataset See more Orthologs mouse all Using only the above description and what you know about the world, is \"The gene A3GALT2 is located in Golgi cisterna membrane.\" definitely correct? Yes or no?", "output": "Yes"}
+{"input": "Given A4GALT, Official Symbol A4GALTprovided by HGNC Official Full Name alpha 1,4-galactosyltransferase (P blood group)provided by HGNC Primary source HGNC:HGNC:18149 See related Ensembl:ENSG00000128274 MIM:607922; AllianceGenome:HGNC:18149 Gene type protein coding RefSeq status REVIEWED Organism Homo sapiens Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known as P1; PK; Gb3S; P(k); P1PK; A14GALT; A4GALT1 Summary The protein encoded by this gene catalyzes the transfer of galactose to lactosylceramide to form globotriaosylceramide, which has been identified as the P(k) antigen of the P blood group system. This protein, a type II membrane protein found in the Golgi, is also required for the synthesis of the bacterial verotoxins receptor. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015] Expression Ubiquitous expression in kidney (RPKM 6.5), fat (RPKM 5.5) and 22 other tissues See more Orthologs mouse all Should we assume that \"A4GALT is a gene.\" is true? Yes or no?", "output": "Yes"}