Datasets:

Aremaki
/

MedMentions

id stringlengths 1 6	document_id stringlengths 8 8	passages listlengths 2 2	entities listlengths 2 136	events listlengths 0 0	coreferences listlengths 0 0	relations listlengths 0 0
0	25763772	[ { "id": "67", "type": "title", "text": [ "DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis" ], "offsets": [ [ 0, 82 ] ] }, { "id": "68", "type": "abstract", "text": [ "Pseudomonas aeruginosa (Pa) infect...	[ { "id": "1", "type": "T103", "text": [ "DCTN4" ], "offsets": [ [ 0, 5 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C4308010" } ] }, { "id": "2", "type": "T038", "text": [ "chronic Pseudomonas a...	[]	[]	[]
69	26316050	[ { "id": "86", "type": "title", "text": [ "Prevascularized silicon membranes for the enhancement of transport to implanted medical devices" ], "offsets": [ [ 0, 95 ] ] }, { "id": "87", "type": "abstract", "text": [ "Recent advances in dr...	[ { "id": "70", "type": "T103", "text": [ "silicon" ], "offsets": [ [ 16, 23 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0037114" } ] }, { "id": "71", "type": "T033", "text": [ "implanted medic...	[]	[]	[]
88	26406200	[ { "id": "137", "type": "title", "text": [ "Seated maximum flexion: An alternative to standing maximum flexion for determining presence of flexion - relaxation?" ], "offsets": [ [ 0, 116 ] ] }, { "id": "138", "type": "abstract", "text": [ ...	[ { "id": "89", "type": "T033", "text": [ "Seated" ], "offsets": [ [ 0, 6 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0277814" } ] }, { "id": "90", "type": "T038", "text": [ "flexion" ], ...	[]	[]	[]
139	26424709	[ { "id": "173", "type": "title", "text": [ "The Relationship Between Distance and Post-operative Visit Attendance Following Medical Male Circumcision in Nyanza Province, Kenya" ], "offsets": [ [ 0, 131 ] ] }, { "id": "174", "type": "abstract", ...	[ { "id": "140", "type": "T033", "text": [ "Post-operative" ], "offsets": [ [ 38, 52 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0241311" } ] }, { "id": "141", "type": "T058", "text": [ "Male C...	[]	[]	[]
175	26476440	[ { "id": "205", "type": "title", "text": [ "Promoting lifestyle behaviour change and well-being in hospital patients: a pilot study of an evidence-based psychological intervention" ], "offsets": [ [ 0, 135 ] ] }, { "id": "206", "type": "abstract",...	[ { "id": "176", "type": "T033", "text": [ "well-being" ], "offsets": [ [ 41, 51 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0424578" } ] }, { "id": "177", "type": "T062", "text": [ "pilot stud...	[]	[]	[]
207	26864880	[ { "id": "247", "type": "title", "text": [ "Combining electrostatic powder with an insecticide: effect on stored - product beetles and on the commodity" ], "offsets": [ [ 0, 107 ] ] }, { "id": "248", "type": "abstract", "text": [ "The op...	[ { "id": "208", "type": "T103", "text": [ "insecticide" ], "offsets": [ [ 39, 50 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0021576" } ] }, { "id": "209", "type": "T204", "text": [ "beetles" ...	[]	[]	[]
249	26867927	[ { "id": "279", "type": "title", "text": [ "Radiofrequency ablation of posteroseptal accessory pathways associated with coronary sinus diverticula" ], "offsets": [ [ 0, 102 ] ] }, { "id": "280", "type": "abstract", "text": [ "Posterosept...	[ { "id": "250", "type": "T058", "text": [ "Radiofrequency ablation" ], "offsets": [ [ 0, 23 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0850292" } ] }, { "id": "251", "type": "T017", "text": [ ...	[]	[]	[]
281	26868132	[ { "id": "336", "type": "title", "text": [ "Association of RBP4 levels with increased arterial stiffness in adolescents with family history of type 2 diabetes" ], "offsets": [ [ 0, 114 ] ] }, { "id": "337", "type": "abstract", "text": [ ...	[ { "id": "282", "type": "T103", "text": [ "RBP4" ], "offsets": [ [ 15, 19 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C1438309" } ] }, { "id": "283", "type": "T038", "text": [ "arterial stiffne...	[]	[]	[]
338	26883265	[ { "id": "411", "type": "title", "text": [ "The effect of total hip arthroplasty on sagittal spinal - pelvic-leg alignment and low back pain in patients with severe hip osteoarthritis" ], "offsets": [ [ 0, 139 ] ] }, { "id": "412", "type": "abstra...	[ { "id": "339", "type": "T058", "text": [ "total hip arthroplasty" ], "offsets": [ [ 14, 36 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0040508" } ] }, { "id": "340", "type": "T082", "text": [ ...	[]	[]	[]
413	26944725	[ { "id": "447", "type": "title", "text": [ "Impact of totally laparoscopic combined management of colorectal cancer with synchronous hepatic metastases on severity of complications: a propensity-score -based analysis" ], "offsets": [ [ 0, 172 ] ] }, { ...	[ { "id": "414", "type": "T058", "text": [ "laparoscopic" ], "offsets": [ [ 18, 30 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0031150" } ] }, { "id": "415", "type": "T038", "text": [ "colorect...	[]	[]	[]
449	27010511	[ { "id": "479", "type": "title", "text": [ "Application of an Analytical Solution as a Screening Tool for Sea Water Intrusion" ], "offsets": [ [ 0, 81 ] ] }, { "id": "480", "type": "abstract", "text": [ "Sea water intrusion into aquifers...	[ { "id": "450", "type": "T058", "text": [ "Screening" ], "offsets": [ [ 43, 52 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0220908" } ] }, { "id": "451", "type": "T170", "text": [ "Tool" ]...	[]	[]	[]
481	27086366	[ { "id": "552", "type": "title", "text": [ "The Role of TRAF4 and B3GAT1 Gene Expression in the Food Hypersensitivity and Insect Venom Allergy in Mastocytosis" ], "offsets": [ [ 0, 114 ] ] }, { "id": "553", "type": "abstract", "text": [ ...	[ { "id": "482", "type": "T017", "text": [ "TRAF4" ], "offsets": [ [ 12, 17 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C1336665" } ] }, { "id": "483", "type": "T017", "text": [ "B3GAT1" ], ...	[]	[]	[]
554	27093899	[ { "id": "584", "type": "title", "text": [ "Generalized Weakness in a Transplant Patient: A Case Presentation" ], "offsets": [ [ 0, 65 ] ] }, { "id": "585", "type": "abstract", "text": [ "Generalized weakness in transplant patients is a ...	[ { "id": "555", "type": "T033", "text": [ "Generalized Weakness" ], "offsets": [ [ 0, 20 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C3714552" } ] }, { "id": "556", "type": "T033", "text": [ "T...	[]	[]	[]
586	27113387	[ { "id": "629", "type": "title", "text": [ "Use of ecoacoustics to determine biodiversity patterns across ecological gradients" ], "offsets": [ [ 0, 82 ] ] }, { "id": "630", "type": "abstract", "text": [ "The variety of local animal soun...	[ { "id": "587", "type": "T082", "text": [ "patterns" ], "offsets": [ [ 46, 54 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0449774" } ] }, { "id": "588", "type": "T082", "text": [ "ecological" ...	[]	[]	[]
631	27121486	[ { "id": "682", "type": "title", "text": [ "Relationship between XspI Site Polymorphisms of LDL-R Gene and Serum IL-2 and IL-10 in Patients with Hypercholesterolemia" ], "offsets": [ [ 0, 121 ] ] }, { "id": "683", "type": "abstract", "text": [...	[ { "id": "632", "type": "T103", "text": [ "XspI" ], "offsets": [ [ 21, 25 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0752931" } ] }, { "id": "633", "type": "T038", "text": [ "Site Polymorphis...	[]	[]	[]
684	27196563	[ { "id": "758", "type": "title", "text": [ "Low serum vitamin D is associated with higher cortical porosity in elderly men" ], "offsets": [ [ 0, 78 ] ] }, { "id": "759", "type": "abstract", "text": [ "Bone loss at peripheral sites in the...	[ { "id": "685", "type": "T031", "text": [ "serum" ], "offsets": [ [ 4, 9 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0229671" } ] }, { "id": "686", "type": "T103", "text": [ "vitamin D" ],...	[]	[]	[]
760	27216824	[ { "id": "818", "type": "title", "text": [ "Rapid Fabrication of a Cell - Seeded Collagen Gel -Based Tubular Construct that Withstands Arterial Pressure: Rapid Fabrication of a Gel -Based Media Equivalent" ], "offsets": [ [ 0, 160 ] ] }, { "id": "819"...	[ { "id": "761", "type": "T017", "text": [ "Cell" ], "offsets": [ [ 23, 27 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0007634" } ] }, { "id": "762", "type": "T058", "text": [ "Seeded" ], ...	[]	[]	[]
820	27233260	[ { "id": "864", "type": "title", "text": [ "Expression and Purification of E2 Glycoprotein from Insect Cells (Sf9) for Use in Serology" ], "offsets": [ [ 0, 90 ] ] }, { "id": "865", "type": "abstract", "text": [ "Chikungunya virus (CHIKV...	[ { "id": "821", "type": "T038", "text": [ "Expression" ], "offsets": [ [ 0, 10 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C1171362" } ] }, { "id": "822", "type": "T058", "text": [ "Purificatio...	[]	[]	[]
866	27233466	[ { "id": "924", "type": "title", "text": [ "Acute risk factors for suicide attempts and death: prospective findings from the STEP - BD study" ], "offsets": [ [ 0, 96 ] ] }, { "id": "925", "type": "abstract", "text": [ "Suicide is unfortu...	[ { "id": "867", "type": "T033", "text": [ "risk factors" ], "offsets": [ [ 6, 18 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0035648" } ] }, { "id": "868", "type": "T033", "text": [ "suicide a...	[]	[]	[]
926	27233592	[ { "id": "947", "type": "title", "text": [ "Measurement of Outcomes of Upper Limb Reconstructive Surgery for Tetraplegia" ], "offsets": [ [ 0, 76 ] ] }, { "id": "948", "type": "abstract", "text": [ "Reconstructive arm/hand surgery for te...	[ { "id": "927", "type": "T038", "text": [ "Tetraplegia" ], "offsets": [ [ 65, 76 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0034372" } ] }, { "id": "928", "type": "T038", "text": [ "tetrapleg...	[]	[]	[]
949	27234004	[ { "id": "999", "type": "title", "text": [ "Factors preventing kneeling in a group of pre-educated patients post total knee arthroplasty" ], "offsets": [ [ 0, 92 ] ] }, { "id": "1000", "type": "abstract", "text": [ "Difficulties in kneel...	[ { "id": "950", "type": "T038", "text": [ "kneeling" ], "offsets": [ [ 19, 27 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C2584307" } ] }, { "id": "951", "type": "T058", "text": [ "total knee a...	[]	[]	[]
1001	27234031	[ { "id": "1048", "type": "title", "text": [ "Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population" ], "offsets": [ [ 0, 140 ] ] }, { "id": "1049", "type": "abs...	[ { "id": "1002", "type": "T033", "text": [ "Improved" ], "offsets": [ [ 0, 8 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0184511" } ] }, { "id": "1003", "type": "T038", "text": [ "neuromuscula...	[]	[]	[]
1050	27235977	[ { "id": "1113", "type": "title", "text": [ "Laser -facilitated epicutaneous immunotherapy to IgE-mediated allergy" ], "offsets": [ [ 0, 69 ] ] }, { "id": "1114", "type": "abstract", "text": [ "Allergen specific immunotherapy has been sh...	[ { "id": "1051", "type": "T058", "text": [ "epicutaneous" ], "offsets": [ [ 19, 31 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C0001558" } ] }, { "id": "1052", "type": "T058", "text": [ "immuno...	[]	[]	[]
1115	27235985	[ { "id": "1148", "type": "title", "text": [ "Predicting real - world functional milestones in schizophrenia" ], "offsets": [ [ 0, 62 ] ] }, { "id": "1149", "type": "abstract", "text": [ "Schizophrenia is a severe disorder that often caus...	[ { "id": "1116", "type": "T098", "text": [ "world" ], "offsets": [ [ 18, 23 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C2700280" } ] }, { "id": "1117", "type": "T038", "text": [ "schizophrenia...	[]	[]	[]
1150	27236033	[ { "id": "1215", "type": "title", "text": [ "LDLR, ApoB and ApoE genes polymorphisms and classical risk factors in premature coronary artery disease" ], "offsets": [ [ 0, 103 ] ] }, { "id": "1216", "type": "abstract", "text": [ "Lipoprot...	[ { "id": "1151", "type": "T017", "text": [ "LDLR" ], "offsets": [ [ 0, 4 ] ], "normalized": [ { "db_name": "UMLS", "db_id": "C1366529" } ] }, { "id": "1152", "type": "T017", "text": [ "ApoB" ], ...	[]	[]	[]

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Dataset Card for MedMentions

MedMentions is a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines.

Corpus: The MedMentions corpus consists of 4,392 papers (Titles and Abstracts) randomly selected from among papers released on PubMed in 2016, that were in the biomedical field, published in the English language, and had both a Title and an Abstract.

Annotators: We recruited a team of professional annotators with rich experience in biomedical content curation to exhaustively annotate all UMLS® (2017AA full version) entity mentions in these papers.

Annotation quality: We did not collect stringent IAA (Inter-annotator agreement) data. To gain insight on the annotation quality of MedMentions, we randomly selected eight papers from the annotated corpus, containing a total of 469 concepts. Two biologists ('Reviewer') who did not participate in the annotation task then each reviewed four papers. The agreement between Reviewers and Annotators, an estimate of the Precision of the annotations, was 97.3%.

Citation Information

@misc{mohan2019medmentions,
      title={MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts},
      author={Sunil Mohan and Donghui Li},
      year={2019},
      eprint={1902.09476},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}