diff --git a/src/model/hint.js b/src/model/hint.js index 404bc948..5a3e3445 100644 --- a/src/model/hint.js +++ b/src/model/hint.js @@ -5,11 +5,11 @@ const HINT_TYPE = Object.freeze({ }); const HINT_TYPES = _.flatMap(HINT_TYPE); -const HINT_PASSAGE = Object.freeze({ +const PASSAGE_TYPE = Object.freeze({ TITLE: 'title', ABSTRACT: 'abstract' }); -const HINT_PASSAGES = _.flatMap(HINT_PASSAGE); +const PASSAGE_TYPES = _.flatMap(PASSAGE_TYPE); /* * Class representing a Hint. @@ -51,7 +51,7 @@ class Hint{ set type(value){ if( value != HINT_TYPES.ORGANISM){ - throw new Error('Invalid type' + value); + throw new TypeError('Invalid type' + value); } this._type = value; } @@ -62,7 +62,7 @@ class Hint{ set xref(value){ if (!value.dbPrefix || !value.id){ - throw new Error('Invalid xref' + JSON.stringify(value)); + throw new TypeError('Invalid xref' + JSON.stringify(value)); } this._xref = value; } @@ -72,14 +72,14 @@ class Hint{ } set section(value){ - if( value != HINT_PASSAGES.TITLE && value != HINT_PASSAGES.ABSTRACT){ - throw new Error('Invalid section' + value); + if( ! _.includes(PASSAGE_TYPES, value) ) { + throw new TypeError('Invalid section' + value); } this._section = value; } } export { Hint, - HINT_TYPES, - HINT_PASSAGES + HINT_TYPE, + PASSAGE_TYPE }; diff --git a/test/pubtator/10.1016_j.molcel.2019.03.023.json b/test/pubtator/10.1016_j.molcel.2019.03.023.json new file mode 100644 index 00000000..dc842a33 --- /dev/null +++ b/test/pubtator/10.1016_j.molcel.2019.03.023.json @@ -0,0 +1,536 @@ +{ + "_id": "31003867|None", + "id": "10.1016/j.molcel.2019.03.023", + "infons": { + "doi": "10.1016/j.molcel.2019.03.023", + "comment": "M. Musculus orthologues: ANKRD31, REC114" + }, + "passages": [ + { + "infons": { + "journal": "Mol Cell. 2019 Jun 6;74(5):1053-1068.e8. doi: 10.1016/j.molcel.2019.03.023. Epub ", + "year": "2019", + "article-id_pmc": "PMC6555648", + "type": "title", + "authors": "Boekhout M, Karasu ME, Wang J, Acquaviva L, Pratto F, Brick K, Eng DY, Xu J, Camerini-Otero RD, Patel DJ, Keeney S" + }, + "offset": 0, + "text": "REC114 Partner ANKRD31 Controls Number, Timing, and Location of Meiotic DNA Breaks.", + "sentences": [], + "annotations": [ + { + "id": "2", + "infons": { + "identifier": "73673", + "type": "Gene", + "ncbi_homologene": "83546", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "text": "REC114", + "locations": [ + { + "offset": 0, + "length": 6 + } + ] + }, + { + "id": "3", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 15, + "length": 7 + } + ] + } + ], + "relations": [] + }, + { + "infons": { + "type": "abstract" + }, + "offset": 84, + "text": "Double-strand breaks (DSBs) initiate the homologous recombination that is crucial for meiotic chromosome pairing and segregation. Here, we unveil mouse ANKRD31 as a lynchpin governing multiple aspects of DSB formation. Spermatocytes lacking ANKRD31 have altered DSB locations and fail to target DSBs to the pseudoautosomal regions (PARs) of sex chromosomes. They also have delayed and/or fewer recombination sites but, paradoxically, more DSBs, suggesting DSB dysregulation. Unrepaired DSBs and pairing failures-stochastic on autosomes, nearly absolute on X and Y-cause meiotic arrest and sterility in males. Ankrd31-deficient females have reduced oocyte reserves. A crystal structure defines a pleckstrin homology (PH) domain in REC114 and its direct intermolecular contacts with ANKRD31. In vivo, ANKRD31 stabilizes REC114 association with the PAR and elsewhere. Our findings inform a model in which ANKRD31 is a scaffold anchoring REC114 and other factors to specific genomic locations, thereby regulating DSB formation.", + "sentences": [], + "annotations": [ + { + "id": "15", + "infons": { + "identifier": "10090", + "type": "Species", + "valid": true, + "normalized": [ + 10090 + ], + "database": "ncbi_taxonomy", + "normalized_id": 10090, + "biotype": "species", + "name": "10090", + "accession": null + }, + "text": "mouse", + "locations": [ + { + "offset": 230, + "length": 5 + } + ] + }, + { + "id": "16", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 236, + "length": 7 + } + ] + }, + { + "id": "17", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 325, + "length": 7 + } + ] + }, + { + "id": "18", + "infons": { + "identifier": "MESH:D007246", + "type": "Disease", + "valid": true, + "normalized": [ + "D007246" + ], + "database": "ncbi_mesh", + "normalized_id": "D007246", + "biotype": "disease", + "name": "Infertility", + "accession": "@DISEASE_Infertility" + }, + "text": "sterility", + "locations": [ + { + "offset": 673, + "length": 9 + } + ] + }, + { + "id": "19", + "infons": { + "identifier": "73673", + "type": "Gene", + "ncbi_homologene": "83546", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "text": "REC114", + "locations": [ + { + "offset": 814, + "length": 6 + } + ] + }, + { + "id": "20", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 865, + "length": 7 + } + ] + }, + { + "id": "21", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 883, + "length": 7 + } + ] + }, + { + "id": "22", + "infons": { + "identifier": "73673", + "type": "Gene", + "ncbi_homologene": "83546", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "text": "REC114", + "locations": [ + { + "offset": 902, + "length": 6 + } + ] + }, + { + "id": "23", + "infons": { + "identifier": "69597", + "type": "Gene", + "ncbi_homologene": "4947", + "valid": true, + "normalized": [ + 69597 + ], + "database": "ncbi_gene", + "normalized_id": 69597, + "biotype": "gene", + "name": "Afg3l2", + "accession": "@GENE_AFG3L2" + }, + "text": "PAR", + "locations": [ + { + "offset": 930, + "length": 3 + } + ] + }, + { + "id": "24", + "infons": { + "identifier": "625662", + "type": "Gene", + "ncbi_homologene": "110355", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "text": "ANKRD31", + "locations": [ + { + "offset": 986, + "length": 7 + } + ] + }, + { + "id": "25", + "infons": { + "identifier": "73673", + "type": "Gene", + "ncbi_homologene": "83546", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "text": "REC114", + "locations": [ + { + "offset": 1018, + "length": 6 + } + ] + } + ], + "relations": [] + } + ], + "relations": [ + { + "id": "R1", + "infons": { + "score": "0.9995", + "role1": { + "identifier": "MESH:D007246", + "type": "Disease", + "valid": true, + "normalized": [ + "D007246" + ], + "database": "ncbi_mesh", + "normalized_id": "D007246", + "biotype": "disease", + "name": "Infertility", + "accession": "@DISEASE_Infertility" + }, + "role2": { + "identifier": "625662", + "type": "Gene", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "0", + "role": "5,4" + } + ] + }, + { + "id": "R2", + "infons": { + "score": "0.9555", + "role1": { + "identifier": "625662", + "type": "Gene", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "role2": { + "identifier": "73673", + "type": "Gene", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "1", + "role": "1,0" + } + ] + }, + { + "id": "R3", + "infons": { + "score": "0.4854", + "role1": { + "identifier": "69597", + "type": "Gene", + "valid": true, + "normalized": [ + 69597 + ], + "database": "ncbi_gene", + "normalized_id": 69597, + "biotype": "gene", + "name": "Afg3l2", + "accession": "@GENE_AFG3L2" + }, + "role2": { + "identifier": "73673", + "type": "Gene", + "valid": true, + "normalized": [ + 73673 + ], + "database": "ncbi_gene", + "normalized_id": 73673, + "biotype": "gene", + "name": "Rec114", + "accession": "@GENE_REC114" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "2", + "role": "10,9" + } + ] + }, + { + "id": "R4", + "infons": { + "score": "0.9952", + "role1": { + "identifier": "625662", + "type": "Gene", + "valid": true, + "normalized": [ + 625662 + ], + "database": "ncbi_gene", + "normalized_id": 625662, + "biotype": "gene", + "name": "Ankrd31", + "accession": "@GENE_ANKRD31" + }, + "role2": { + "identifier": "69597", + "type": "Gene", + "valid": true, + "normalized": [ + 69597 + ], + "database": "ncbi_gene", + "normalized_id": 69597, + "biotype": "gene", + "name": "Afg3l2", + "accession": "@GENE_AFG3L2" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "3", + "role": "8,10" + } + ] + } + ], + "pmid": 31003867, + "pmcid": null, + "meta": {}, + "date": "2019-06-06T00:00:00Z", + "journal": "Mol Cell", + "authors": [ + "Boekhout M", + "Karasu ME", + "Wang J", + "Acquaviva L", + "Pratto F", + "Brick K", + "Eng DY", + "Xu J", + "Camerini-Otero RD", + "Patel DJ", + "Keeney S" + ], + "relations_display": [ + { + "name": "associate|@DISEASE_Infertility|@GENE_ANKRD31" + }, + { + "name": "associate|@GENE_ANKRD31|@GENE_REC114" + }, + { + "name": "associate|@GENE_AFG3L2|@GENE_REC114" + }, + { + "name": "associate|@GENE_ANKRD31|@GENE_AFG3L2" + } + ] + } \ No newline at end of file diff --git a/test/pubtator/10.1016_j.molcel.2024.01.007.json b/test/pubtator/10.1016_j.molcel.2024.01.007.json new file mode 100644 index 00000000..b837a397 --- /dev/null +++ b/test/pubtator/10.1016_j.molcel.2024.01.007.json @@ -0,0 +1,497 @@ +{ + "_id": "38309274|None", + "id": "10.1016/j.molcel.2024.01.007", + "infons": { + "doi": "10.1016/j.molcel.2024.01.007", + "comment": "Get: Missing IκBζ; mapping greek symbol" + }, + "passages": [ + { + "infons": { + "journal": "Mol Cell;2024Jan24. doi:10.1016/j.molcel.2024.01.007", + "year": "2024", + "type": "title", + "authors": "Alpsoy A, Wu XS, Pal S, Klingbeil O, Kumar P, El Demerdash O, Nalbant B, Vakoc CR, " + }, + "offset": 0, + "text": "IkappaBzeta is a dual-use coactivator of NF-kappaB and POU transcription factors.", + "sentences": [], + "annotations": [ + { + "id": "2", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 0, + "length": 11 + } + ] + }, + { + "id": "3", + "infons": { + "identifier": "4790", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 41, + "length": 9 + } + ] + } + ], + "relations": [] + }, + { + "infons": { + "type": "abstract" + }, + "offset": 82, + "text": "OCA-B, OCA-T1, and OCA-T2 belong to a family of coactivators that bind to POU transcription factors (TFs) to regulate gene expression in immune cells. Here, we identify IkappaBzeta (encoded by the NFKBIZ gene) as an additional coactivator of POU TFs. Although originally discovered as an inducible regulator of NF-kappaB, we show here that IkappaBzeta shares a microhomology with OCA proteins and uses this segment to bind to POU TFs and octamer-motif-containing DNA. Our functional experiments suggest that IkappaBzeta requires its interaction with POU TFs to coactivate immune-related genes. This finding is reinforced by epigenomic analysis of MYD88L265P-mutant lymphoma cells, which revealed colocalization of IkappaBzeta with the POU TF OCT2 and NF-kappaB:p50 at hundreds of DNA elements harboring octamer and kappaB motifs. These results suggest that IkappaBzeta is a transcriptional coactivator that can amplify and integrate the output of NF-kappaB and POU TFs at inducible genes in immune cells.", + "sentences": [], + "annotations": [ + { + "id": "17", + "infons": { + "identifier": "5450", + "type": "Gene", + "ncbi_homologene": "4543", + "valid": true, + "normalized": [ + 5450 + ], + "database": "ncbi_gene", + "normalized_id": 5450, + "biotype": "gene", + "name": "POU2AF1", + "accession": "@GENE_POU2AF1" + }, + "text": "OCA-B", + "locations": [ + { + "offset": 82, + "length": 5 + } + ] + }, + { + "id": "18", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 251, + "length": 11 + } + ] + }, + { + "id": "19", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "NFKBIZ", + "locations": [ + { + "offset": 279, + "length": 6 + } + ] + }, + { + "id": "20", + "infons": { + "identifier": "4790", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 393, + "length": 9 + } + ] + }, + { + "id": "21", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 422, + "length": 11 + } + ] + }, + { + "id": "22", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 590, + "length": 11 + } + ] + }, + { + "id": "23", + "infons": { + "identifier": "MESH:D008223", + "type": "Disease", + "valid": true, + "normalized": [ + "D008223" + ], + "database": "ncbi_mesh", + "normalized_id": "D008223", + "biotype": "disease", + "name": "Lymphoma", + "accession": "@DISEASE_Lymphoma" + }, + "text": "lymphoma", + "locations": [ + { + "offset": 747, + "length": 8 + } + ] + }, + { + "id": "24", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 796, + "length": 11 + } + ] + }, + { + "id": "25", + "infons": { + "identifier": "5452", + "type": "Gene", + "ncbi_homologene": "55674", + "valid": true, + "normalized": [ + 5452 + ], + "database": "ncbi_gene", + "normalized_id": 5452, + "biotype": "gene", + "name": "POU2F2", + "accession": "@GENE_POU2F2" + }, + "text": "OCT2", + "locations": [ + { + "offset": 824, + "length": 4 + } + ] + }, + { + "id": "26", + "infons": { + "identifier": "4790", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 833, + "length": 9 + } + ] + }, + { + "id": "27", + "infons": { + "identifier": "4790", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "text": "p50", + "locations": [ + { + "offset": 843, + "length": 3 + } + ] + }, + { + "id": "28", + "infons": { + "identifier": "64332", + "type": "Gene", + "ncbi_homologene": "12734", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "text": "IkappaBzeta", + "locations": [ + { + "offset": 939, + "length": 11 + } + ] + }, + { + "id": "29", + "infons": { + "identifier": "4790", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 1029, + "length": 9 + } + ] + } + ], + "relations": [] + } + ], + "relations": [ + { + "id": "R1", + "infons": { + "score": "0.9989", + "role1": { + "identifier": "5452", + "type": "Gene", + "valid": true, + "normalized": [ + 5452 + ], + "database": "ncbi_gene", + "normalized_id": 5452, + "biotype": "gene", + "name": "POU2F2", + "accession": "@GENE_POU2F2" + }, + "role2": { + "identifier": "64332", + "type": "Gene", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "0", + "role": "10,9" + } + ] + }, + { + "id": "R2", + "infons": { + "score": "0.9979", + "role1": { + "identifier": "4790", + "type": "Gene", + "valid": true, + "normalized": [ + 4790 + ], + "database": "ncbi_gene", + "normalized_id": 4790, + "biotype": "gene", + "name": "NFKB1", + "accession": "@GENE_NFKB1" + }, + "role2": { + "identifier": "64332", + "type": "Gene", + "valid": true, + "normalized": [ + 64332 + ], + "database": "ncbi_gene", + "normalized_id": 64332, + "biotype": "gene", + "name": "NFKBIZ", + "accession": "@GENE_NFKBIZ" + }, + "type": "Positive_Correlation" + }, + "nodes": [ + { + "refid": "1", + "role": "1,0" + } + ] + } + ], + "pmid": 38309274, + "pmcid": null, + "meta": {}, + "date": "2024-01-24T00:00:00Z", + "journal": "Mol Cell", + "authors": [ + "Alpsoy A", + "Wu XS", + "Pal S", + "Klingbeil O", + "Kumar P", + "El Demerdash O", + "Nalbant B", + "Vakoc CR" + ], + "relations_display": [ + { + "name": "associate|@GENE_POU2F2|@GENE_NFKBIZ" + }, + { + "name": "positive_correlate|@GENE_NFKB1|@GENE_NFKBIZ" + } + ] + } \ No newline at end of file diff --git a/test/pubtator/10.1038_s41556-021-00642-9.json b/test/pubtator/10.1038_s41556-021-00642-9.json new file mode 100644 index 00000000..87a81787 --- /dev/null +++ b/test/pubtator/10.1038_s41556-021-00642-9.json @@ -0,0 +1,770 @@ +{ + "_id": "33664495|None", + "id": "10.1038/s41556-021-00642-9", + "infons": { + "doi": "10.1038/s41556-021-00642-9", + "comment": "M. musculus orthologue: Aida, Ucp1" + }, + "passages": [ + { + "infons": { + "journal": "Nat Cell Biol. 2021 Mar;23(3):268-277. doi: 10.1038/s41556-021-00642-9. Epub 2021 ", + "year": "2021", + "type": "title", + "authors": "Shi M, Huang XY, Ren XY, Wei XY, Ma Y, Lin ZZ, Liu DT, Song L, Zhao TJ, Li G, Yao L, Zhu M, Zhang C, Xie C, Wu Y, Wu HM, Fan LP, Ou J, Zhan YH, Lin SY, Lin SC" + }, + "offset": 0, + "text": "AIDA directly connects sympathetic innervation to adaptive thermogenesis by UCP1.", + "sentences": [], + "annotations": [ + { + "id": "2", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 0, + "length": 4 + } + ] + }, + { + "id": "3", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 76, + "length": 4 + } + ] + } + ], + "relations": [] + }, + { + "infons": { + "type": "abstract" + }, + "offset": 82, + "text": "The sympathetic nervous system-catecholamine-uncoupling protein 1 (UCP1) axis plays an essential role in non-shivering adaptive thermogenesis. However, whether there exists a direct effector that physically connects catecholamine signalling to UCP1 in response to acute cold is unknown. Here we report that outer mitochondrial membrane-located AIDA is phosphorylated at S161 by the catecholamine-activated protein kinase A (PKA). Phosphorylated AIDA translocates to the intermembrane space, where it binds to and activates the uncoupling activity of UCP1 by promoting cysteine oxidation of UCP1. Adipocyte-specific depletion of AIDA abrogates UCP1-dependent thermogenesis, resulting in hypothermia during acute cold exposure. Re-expression of S161A-AIDA, unlike wild-type AIDA, fails to restore the acute cold response in Aida-knockout mice. The PKA-AIDA-UCP1 axis is highly conserved in mammals, including hibernators. Denervation of the sympathetic postganglionic fibres abolishes cold-induced AIDA-dependent thermogenesis. These findings uncover a direct mechanistic link between sympathetic input and UCP1-mediated adaptive thermogenesis.", + "sentences": [], + "annotations": [ + { + "id": "25", + "infons": { + "identifier": "MESH:D002395", + "type": "Chemical", + "valid": true, + "normalized": [ + "D002395" + ], + "database": "ncbi_mesh", + "normalized_id": "D002395", + "biotype": "chemical", + "name": "Catecholamines", + "accession": "@CHEMICAL_Catecholamines" + }, + "text": "catecholamine", + "locations": [ + { + "offset": 113, + "length": 13 + } + ] + }, + { + "id": "26", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 149, + "length": 4 + } + ] + }, + { + "id": "27", + "infons": { + "identifier": "MESH:D002395", + "type": "Chemical", + "valid": true, + "normalized": [ + "D002395" + ], + "database": "ncbi_mesh", + "normalized_id": "D002395", + "biotype": "chemical", + "name": "Catecholamines", + "accession": "@CHEMICAL_Catecholamines" + }, + "text": "catecholamine", + "locations": [ + { + "offset": 298, + "length": 13 + } + ] + }, + { + "id": "28", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 326, + "length": 4 + } + ] + }, + { + "id": "29", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 426, + "length": 4 + } + ] + }, + { + "id": "30", + "infons": { + "identifier": "tmVar:p|Allele|S|161;VariantGroup:0;OriginalGene:108909;CorrespondingGene:64853;CorrespondingSpecies:10090", + "type": "Variant", + "valid": true, + "subtype": "ProteinMutation", + "database": "litvar", + "original_genes_ids": [ + 108909 + ], + "original_gene_id": 108909, + "gene_ids": [ + 64853 + ], + "gene_id": 64853, + "species_ids": [ + 10090 + ], + "species_id": 10090, + "rsids": [], + "normalized": [ + "#64853#", + "#64853#" + ], + "normalized_id": "#64853#", + "biotype": "variant", + "name": "#64853#", + "accession": null + }, + "text": "S161", + "locations": [ + { + "offset": 452, + "length": 4 + } + ] + }, + { + "id": "31", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 527, + "length": 4 + } + ] + }, + { + "id": "32", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 632, + "length": 4 + } + ] + }, + { + "id": "33", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 672, + "length": 4 + } + ] + }, + { + "id": "34", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 710, + "length": 4 + } + ] + }, + { + "id": "35", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 725, + "length": 4 + } + ] + }, + { + "id": "36", + "infons": { + "identifier": "MESH:D007035", + "type": "Disease", + "valid": true, + "normalized": [ + "D007035" + ], + "database": "ncbi_mesh", + "normalized_id": "D007035", + "biotype": "disease", + "name": "Hypothermia", + "accession": "@DISEASE_Hypothermia" + }, + "text": "hypothermia", + "locations": [ + { + "offset": 768, + "length": 11 + } + ] + }, + { + "id": "37", + "infons": { + "identifier": "tmVar:p|SUB|S|161|A;HGVS:p.S161A;VariantGroup:0;OriginalGene:108909;CorrespondingGene:64853;CorrespondingSpecies:10090", + "type": "Variant", + "valid": true, + "subtype": "ProteinMutation", + "database": "litvar", + "hgvs": "p.S161A", + "original_genes_ids": [ + 108909 + ], + "original_gene_id": 108909, + "gene_ids": [ + 64853 + ], + "gene_id": 64853, + "species_ids": [ + 10090 + ], + "species_id": 10090, + "rsids": [], + "normalized": [ + "#64853#p.S161A", + "#64853#" + ], + "normalized_id": "#64853#p.S161A", + "biotype": "variant", + "name": "p.S161A", + "accession": "@VARIANT_p.S161A_AIDA_human" + }, + "text": "S161A", + "locations": [ + { + "offset": 825, + "length": 5 + } + ] + }, + { + "id": "38", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 831, + "length": 4 + } + ] + }, + { + "id": "39", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 854, + "length": 4 + } + ] + }, + { + "id": "40", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "Aida", + "locations": [ + { + "offset": 904, + "length": 4 + } + ] + }, + { + "id": "41", + "infons": { + "identifier": "10090", + "type": "Species", + "valid": true, + "normalized": [ + 10090 + ], + "database": "ncbi_taxonomy", + "normalized_id": 10090, + "biotype": "species", + "name": "10090", + "accession": null + }, + "text": "mice", + "locations": [ + { + "offset": 918, + "length": 4 + } + ] + }, + { + "id": "42", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 932, + "length": 4 + } + ] + }, + { + "id": "43", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 937, + "length": 4 + } + ] + }, + { + "id": "44", + "infons": { + "identifier": "108909", + "type": "Gene", + "ncbi_homologene": "11268", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "text": "AIDA", + "locations": [ + { + "offset": 1078, + "length": 4 + } + ] + }, + { + "id": "45", + "infons": { + "identifier": "22227", + "type": "Gene", + "ncbi_homologene": "22524", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "text": "UCP1", + "locations": [ + { + "offset": 1187, + "length": 4 + } + ] + } + ], + "relations": [] + } + ], + "relations": [ + { + "id": "R1", + "infons": { + "score": "0.7694", + "role1": { + "identifier": "108909", + "type": "Gene", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "role2": { + "identifier": "22227", + "type": "Gene", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "type": "Positive_Correlation" + }, + "nodes": [ + { + "refid": "0", + "role": "0,1" + } + ] + }, + { + "id": "R2", + "infons": { + "score": "0.9975", + "role1": { + "identifier": "MESH:D007035", + "type": "Disease", + "valid": true, + "normalized": [ + "D007035" + ], + "database": "ncbi_mesh", + "normalized_id": "D007035", + "biotype": "disease", + "name": "Hypothermia", + "accession": "@DISEASE_Hypothermia" + }, + "role2": { + "identifier": "108909", + "type": "Gene", + "valid": true, + "normalized": [ + 108909 + ], + "database": "ncbi_gene", + "normalized_id": 108909, + "biotype": "gene", + "name": "Aida", + "accession": "@GENE_AIDA" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "1", + "role": "13,11" + } + ] + }, + { + "id": "R3", + "infons": { + "score": "0.9889", + "role1": { + "identifier": "MESH:D002395", + "type": "Chemical", + "valid": true, + "normalized": [ + "D002395" + ], + "database": "ncbi_mesh", + "normalized_id": "D002395", + "biotype": "chemical", + "name": "Catecholamines", + "accession": "@CHEMICAL_Catecholamines" + }, + "role2": { + "identifier": "22227", + "type": "Gene", + "valid": true, + "normalized": [ + 22227 + ], + "database": "ncbi_gene", + "normalized_id": 22227, + "biotype": "gene", + "name": "Ucp1", + "accession": "@GENE_UCP1" + }, + "type": "Association" + }, + "nodes": [ + { + "refid": "2", + "role": "2,3" + } + ] + } + ], + "pmid": 33664495, + "pmcid": null, + "meta": {}, + "date": "2021-03-01T00:00:00Z", + "journal": "Nat Cell Biol", + "authors": [ + "Shi M", + "Huang XY", + "Ren XY", + "Wei XY", + "Ma Y", + "Lin ZZ", + "Liu DT", + "Song L", + "Zhao TJ", + "Li G", + "Yao L", + "Zhu M", + "Zhang C", + "Xie C", + "Wu Y", + "Wu HM", + "Fan LP", + "Ou J", + "Zhan YH", + "Lin SY", + "Lin SC" + ], + "relations_display": [ + { + "name": "positive_correlate|@GENE_AIDA|@GENE_UCP1" + }, + { + "name": "associate|@DISEASE_Hypothermia|@GENE_AIDA" + }, + { + "name": "associate|@CHEMICAL_Catecholamines|@GENE_UCP1" + } + ] + } \ No newline at end of file diff --git a/test/pubtator/10.1126_scisignal.abf3535.json b/test/pubtator/10.1126_scisignal.abf3535.json new file mode 100644 index 00000000..fc88421a --- /dev/null +++ b/test/pubtator/10.1126_scisignal.abf3535.json @@ -0,0 +1,1482 @@ +{ + "_id": "34546791|None", + "id": "10.1126/scisignal.abf3535", + "infons": { + "doi": "10.1126/scisignal.abf3535", + "comment": "Synonym + ortholog: p50, p65; red-herring: NF-kappaB; title organism; IL-1beta totally buried" + }, + "passages": [ + { + "infons": { + "journal": "Sci Signal. 2021 Sep 21;14(701):eabf3535. doi: 10.1126/scisignal.abf3535. Epub ", + "year": "2021", + "article-id_pmc": "PMC8734558", + "type": "title", + "authors": "Catheline SE, Bell RD, Oluoch LS, James MN, Escalera-Rivera K, Maynard RD, Chang ME, Dean C, Botto E, Ketz JP, Boyce BF, Zuscik MJ, Jonason JH" + }, + "offset": 0, + "text": "IKKbeta-NF-kappaB signaling in adult chondrocytes promotes the onset of age-related osteoarthritis in mice.", + "sentences": [], + "annotations": [ + { + "id": "4", + "infons": { + "identifier": "16150", + "type": "Gene", + "ncbi_homologene": "7782", + "valid": true, + "normalized": [ + 16150 + ], + "database": "ncbi_gene", + "normalized_id": 16150, + "biotype": "gene", + "name": "Ikbkb", + "accession": "@GENE_IKBKB" + }, + "text": "IKKbeta", + "locations": [ + { + "offset": 0, + "length": 7 + } + ] + }, + { + "id": "5", + "infons": { + "identifier": "18033", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 18033 + ], + "database": "ncbi_gene", + "normalized_id": 18033, + "biotype": "gene", + "name": "Nfkb1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 8, + "length": 9 + } + ] + }, + { + "id": "6", + "infons": { + "identifier": "MESH:D010003", + "type": "Disease", + "valid": true, + "normalized": [ + "D010003" + ], + "database": "ncbi_mesh", + "normalized_id": "D010003", + "biotype": "disease", + "name": "Osteoarthritis", + "accession": "@DISEASE_Osteoarthritis" + }, + "text": "osteoarthritis", + "locations": [ + { + "offset": 84, + "length": 14 + } + ] + }, + { + "id": "7", + "infons": { + "identifier": "10090", + "type": "Species", + "valid": true, + "normalized": [ + 10090 + ], + "database": "ncbi_taxonomy", + "normalized_id": 10090, + "biotype": "species", + "name": "10090", + "accession": null + }, + "text": "mice", + "locations": [ + { + "offset": 102, + "length": 4 + } + ] + } + ], + "relations": [] + }, + { + "infons": { + "type": "abstract" + }, + "offset": 108, + "text": "Canonical nuclear factor kappaB (NF-kappaB) signaling mediated by homo- and heterodimers of the NF-kappaB subunits p65 (RELA) and p50 (NFKB1) is associated with age-related pathologies and with disease progression in posttraumatic models of osteoarthritis (OA). Here, we established that NF-kappaB signaling in articular chondrocytes increased with age, concomitant with the onset of spontaneous OA in wild-type mice. Chondrocyte-specific expression of a constitutively active form of inhibitor of kappaB kinase beta (IKKbeta) in young adult mice accelerated the onset of the OA-like phenotype observed in aging wild-type mice, including degenerative changes in the articular cartilage, synovium, and menisci. Both in vitro and in vivo, chondrocytes expressing activated IKKbeta had a proinflammatory secretory phenotype characterized by markers typically associated with the senescence-associated secretory phenotype (SASP). Expression of these factors was differentially regulated by p65, which contains a transactivation domain, and p50, which does not. Whereas the loss of p65 blocked the induction of genes encoding SASP factors in chondrogenic cells treated with interleukin-1beta (IL-1beta) in vitro, the loss of p50 enhanced the IL-1beta-induced expression of some SASP factors. The loss of p50 further exacerbated cartilage degeneration in mice with chondrocyte-specific IKKbeta activation. Overall, our data reveal that IKKbeta-mediated activation of p65 can promote OA onset and that p50 may limit cartilage degeneration in settings of joint inflammation including advanced age.", + "sentences": [], + "annotations": [ + { + "id": "45", + "infons": { + "identifier": "18033", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 18033 + ], + "database": "ncbi_gene", + "normalized_id": 18033, + "biotype": "gene", + "name": "Nfkb1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 141, + "length": 9 + } + ] + }, + { + "id": "46", + "infons": { + "identifier": "18033", + "type": "Gene", + "ncbi_homologene": "2971", + "valid": true, + "normalized": [ + 18033 + ], + "database": "ncbi_gene", + "normalized_id": 18033, + "biotype": "gene", + "name": "Nfkb1", + "accession": "@GENE_NFKB1" + }, + "text": "NF-kappaB", + "locations": [ + { + "offset": 204, + "length": 9 + } + ] + }, + { + "id": "47", + "infons": { + 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C", + "Botto E", + "Ketz JP", + "Boyce BF", + "Zuscik MJ", + "Jonason JH" + ], + "relations_display": [ + { + "name": "associate|@DISEASE_Osteoarthritis|@GENE_NFKB1" + }, + { + "name": "associate|@DISEASE_Cartilage_Diseases|@GENE_IKBKB" + }, + { + "name": "positive_correlate|@GENE_IKBKB|@GENE_RELA" + }, + { + "name": "interact|@GENE_NFKB1|@GENE_RELA" + }, + { + "name": "inhibit|@DISEASE_Cartilage_Diseases|@GENE_NFKB1" + }, + { + "name": "associate|@GENE_IKBKB|@GENE_NFKB1" + }, + { + "name": "negative_correlate|@GENE_IL1B|@GENE_NFKB1" + }, + { + "name": "associate|@DISEASE_Osteoarthritis|@GENE_IKBKB" + }, + { + "name": "associate|@DISEASE_Osteoarthritis|@GENE_RELA" + }, + { + "name": "associate|@DISEASE_Inflammation|@GENE_NFKB1" + }, + { + "name": "associate|@DISEASE_Nephrosis_Lipoid|@GENE_IKBKB" + } + ] + } \ No newline at end of file diff --git a/test/pubtator/10.15252_embj.2023113616.json b/test/pubtator/10.15252_embj.2023113616.json new file mode 100644 index 00000000..c42db5ee --- /dev/null +++ b/test/pubtator/10.15252_embj.2023113616.json @@ -0,0 +1,236 @@ +{ + "_id": "37317646|None", + "id": "10.15252/embj.2023113616", + "infons": { + "doi": "10.15252/embj.2023113616", + "comment": "Human, fly and worm (multiple, erroneous IDs) where human is not priority and others are equal" + }, + "passages": [ + { + "infons": { + "journal": "EMBO J;2023Jun15 113616. doi:10.15252/embj.2023113616", + "year": "2023", + "article-id_pmc": "PMC10425847", + "type": "title", + "authors": "Dobbelaere J, Su TY, Erdi B, Schleiffer A, Dammermann A, " + }, + "offset": 0, + "text": "A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans.", + "sentences": [], + "annotations": [ + { + "id": "2", + "infons": { + "identifier": "7227", + "type": "Species", + "valid": true, + "normalized": [ + 7227 + ], + "database": "ncbi_taxonomy", + "normalized_id": 7227, + "biotype": "species", + "name": "7227", + "accession": null + }, + "text": "Drosophila", + "locations": [ + { + "offset": 73, + "length": 10 + } + ] + }, + { + "id": "3", + "infons": { + "identifier": "6239;252961;314391;316080", + "type": "Species", + "valid": true, + "normalized": [ + 6239 + ], + "database": "ncbi_taxonomy", + "normalized_id": 6239, + "biotype": "species", + "name": "6239", + "accession": null + }, + "text": "C. elegans", + "locations": [ + { + "offset": 88, + "length": 10 + } + ] + } + ], + "relations": [] + }, + { + "infons": { + "type": "abstract" + }, + "offset": 100, + "text": "Cilia are cellular projections that perform sensory and motile functions in eukaryotic cells. A defining feature of cilia is that they are evolutionarily ancient, yet not universally conserved. In this study, we have used the resulting presence and absence pattern in the genomes of diverse eukaryotes to identify a set of 386 human genes associated with cilium assembly or motility. Comprehensive tissue-specific RNAi in Drosophila and mutant analysis in C. elegans revealed signature ciliary defects for 70-80% of novel genes, a percentage similar to that for known genes within the cluster. Further characterization identified different phenotypic classes, including a set of genes related to the cartwheel component Bld10/CEP135 and two highly conserved regulators of cilium biogenesis. We propose this dataset defines the core set of genes required for cilium assembly and motility across eukaryotes and presents a valuable resource for future studies of cilium biology and associated disorders.", + "sentences": [], + "annotations": [ + { + "id": "10", + "infons": { + "identifier": "9606", + "type": "Species", + "valid": true, + "normalized": [ + 9606 + ], + "database": "ncbi_taxonomy", + "normalized_id": 9606, + "biotype": "species", + "name": "9606", + "accession": null + }, + "text": "human", + "locations": [ + { + "offset": 427, + "length": 5 + } + ] + }, + { + "id": "11", + "infons": { + "identifier": "7227", + "type": "Species", + "valid": true, + "normalized": [ + 7227 + ], + "database": "ncbi_taxonomy", + "normalized_id": 7227, + "biotype": "species", + "name": "7227", + "accession": null + }, + "text": "Drosophila", + "locations": [ + { + "offset": 522, + "length": 10 + } + ] + }, + { + "id": "12", + "infons": { + "identifier": "6239;252961;314391;316080", + "type": "Species", + "valid": true, + "normalized": [ + 6239 + ], + "database": "ncbi_taxonomy", + "normalized_id": 6239, + "biotype": "species", + "name": "6239", + "accession": null + }, + "text": "C. elegans", + "locations": [ + { + "offset": 556, + "length": 10 + } + ] + }, + { + "id": "13", + "infons": { + "identifier": "MESH:D002925", + "type": "Disease", + "valid": true, + "normalized": [ + "D002925" + ], + "database": "ncbi_mesh", + "normalized_id": "D002925", + "biotype": "disease", + "name": "Ciliary Motility Disorders", + "accession": "@DISEASE_Ciliary_Motility_Disorders" + }, + "text": "ciliary defects", + "locations": [ + { + "offset": 586, + "length": 15 + } + ] + }, + { + "id": "14", + "infons": { + "identifier": "39647", + "type": "Gene", + "ncbi_homologene": "45709", + "valid": true, + "normalized": [ + 39647 + ], + "database": "ncbi_gene", + "normalized_id": 39647, + "biotype": "gene", + "name": "Cep135", + "accession": "@GENE_CEP135" + }, + "text": "Bld10", + "locations": [ + { + "offset": 820, + "length": 5 + } + ] + }, + { + "id": "15", + "infons": { + "identifier": "9662", + "type": "Gene", + "ncbi_homologene": "45709", + "valid": true, + "normalized": [ + 9662 + ], + "database": "ncbi_gene", + "normalized_id": 9662, + "biotype": "gene", + "name": "CEP135", + "accession": "@GENE_CEP135" + }, + "text": "CEP135", + "locations": [ + { + "offset": 826, + "length": 6 + } + ] + } + ], + "relations": [] + } + ], + "relations": [], + "pmid": 37317646, + "pmcid": null, + "meta": {}, + "date": "2023-06-15T00:00:00Z", + "journal": "EMBO J", + "authors": [ + "Dobbelaere J", + "Su TY", + "Erdi B", + "Schleiffer A", + "Dammermann A" + ], + "relations_display": [] +} \ No newline at end of file diff --git a/test/pubtator/pubtator.js b/test/pubtator/pubtator.js new file mode 100644 index 00000000..f5114efe --- /dev/null +++ b/test/pubtator/pubtator.js @@ -0,0 +1,25 @@ +import { pubtator_2 } from './10.1016_j.molcel.2019.03.023.json'; +import { pubtator_4 } from './10.1016_j.molcel.2024.01.007.json'; +import { pubtator_5 } from './10.1038_s41556-021-00642-9.json'; +import { pubtator_6 } from './10.1126_scisignal.abf3535.json'; +import { pubtator_7 } from './10.15252_embj.2023113616.json'; + +/** + * bioCDocuments + * + * This is an array of object documents that have set of fields { _id, infons, passages, relations, pmid, etc. } + * A passage is and array of 2 objects, each object is either of type: { title or abstract }, and has an + * annotations array of objects where each object indicates the id and the type of the bioentity (i.e gene, species, etc). +*/ +const bioCDocuments = [ + //0..1 + pubtator_2, // pmid: 31003867 | 0 organism hints in title { } | 1 organism hints in abstract: { 10090 aka (Mus musculus): 1 } | text: [ [] , ["mouse"] ] + //0..0 + pubtator_4, // pmid: 38309274 | 0 organism hints in title { } | 0 organism hints in abstract: { } | text: [ [] , [] ] + //0..1 + pubtator_5, // pmid: 33664495 | 0 organism hints in title { } | 1 organism hints in abstract: { 10090 aka (Mus musculus): 1 } | text: [ [] , ["mice"] ] + //1..* + pubtator_6, // pmid: 34546791 | 1 organism hints in title { 10090 aka (Mus musculus): 1 } | 4 organism hints in abstract: { 10090 aka (Mus musculus): 1 } | text: [ ["mice"] , ["mice" , "mice" , "mice" , "mice"] ] + //*..* + pubtator_7 // pmid: 37317646 | 2 organism hints in title { 7227 aka (Drosophila melanogaster): 1 , 6239 aka (Caeonorhabditis elegans): 1 } | 3 organism hints in abstract: { 9606 aka (Homo sapiens): 1 , 7227 aka (Drosophila melanogaster): 1 , 6239 aka (Caeonorhabditis elegans): 1 } | text: [ [ "Drosophila" , "C. elegans"] , [ "human" , "Drosophila" , "C. elegans" ] ] + ]; \ No newline at end of file