{ "bcoid": "GLY_000470", "title": "SARS-CoV2 Protein Citations (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information ...", "filename": "sarscov2_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "A new corona..." ], [ "P0DTD2-1...", "SARS-CoV-2 O..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "P0DTD2-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTD2" ], [ "P0DTD2-1", "SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70.", "Cell. Mol. Immunol.", "2020", "Li Y., Zhang J., Chen H., Xie J., Han Z.G., Qi H., Wang X.N., Jiang H.W., Meng Q.F., Tao S.C., Wang P.H., Zhang H.N., Zheng Y.X.", "protein_xref_pubmed", "32728199", "protein_xref_uniprotkb", "P0DTD2" ], [ "A0A663DJA2-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "A0A663DJA2-1", "Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Northern Germany.", "Microbiol. Resour. Announc.", "2020", "Huang J., Aepfelbacher M., Fischer N., Gunther T., Pfefferle S., Grundhoff A., Indenbirken D., Lutgehetmann M., Norz D., Oestereich L.", "protein_xref_pubmed", "32499358", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "A0A663DJA2-1", "Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis.", "Nat. Commun.", "2020", "Meier C., Ferron F., Canard B., Decroly E., Le N.T., Coutard B., Selisko B., Fattorini V., Huchting J., Peersen O., Piorkowski G., Shannon A., Touret F.", "protein_xref_pubmed", "32943628", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "A0A663DJA2-1", "Cold-Adapted Live Attenuated SARS-Cov-2 Vaccine Completely Protects Human ACE2 Transgenic Mice from SARS-Cov-2 Infection.", "Vaccines (Basel)", "2020", "Seo S.H., Jang Y.", "protein_xref_pubmed", "33022950", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "A0A663DJA2-1", "Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China.", "Emerg. Infect. Dis.", "2021", "Yip S.P., Que T.L., Wong B.K., Liu R.W., Chan M.C., Chau S.K., Choi M.P., Fung K.S., Lao H.Y., Lee L.K., Leung K.S., Leung W.S., Lung K.C., Man Ho A.Y., Ng T.T., Ng Y.Y., Shum D.H., Sin K.M., Siu G.K., Tam K.K., To W.K., Tso E.Y., Wu A.K., Yam W.C., Yau M.C., Yip K.T.", "protein_xref_pubmed", "33350913", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "A0A663DJA2-1", "An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa.", "MSphere", "2021", "Fischer C., Nagel M., Drosten C., Aissi M.A.J., Akogbeto P., Badou Y., Brunink S., Dossou A., Drexler J.F., F de Oliveira Filho E., Harouna Djingarey M., Hounkanrin G., Hounkpatin B., Krause N., Moreira-Soto A., Sander A.L., Tchibozo C., Yadouleton A.", "protein_xref_pubmed", "33441410", "protein_xref_uniprotkb", "A0A663DJA2" ], [ "P0DTG1-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTG1" ], [ "P0DTG1-1", "Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses.", "Infect. Genet. Evol.", "2020", "Cagliani R., Sironi M., Clerici M., Forni D.", "protein_xref_pubmed", "32387562", "protein_xref_uniprotkb", "P0DTG1" ], [ "P0DTG1-1", "A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a.", "J. Gen. Virol.", "2020", "Firth A.E.", "protein_xref_pubmed", "32667280", "protein_xref_uniprotkb", "P0DTG1" ], [ "P0DTD3-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTD3" ], [ "P0DTD3-1", "Characterization of accessory genes in coronavirus genomes.", "Virol. J.", "2020", "Poch O., Mayer C., Thompson J.D., Michel C.J.", "protein_xref_pubmed", "32854725", "protein_xref_uniprotkb", "P0DTD3" ], [ "P0DTC7-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC7" ], [ "P0DTC7-1", "Ubiquitination of SARS-CoV-2 ORF7a promotes antagonism of interferon response.", "Cell. Mol. Immunol.", "2021", "Wang H., Cao Z., Xia H., Xia X., Shi P.Y., Rajsbaum R.", "protein_xref_pubmed", "33473190", "protein_xref_uniprotkb", "P0DTC7" ], [ "P0DTC6-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC6" ], [ "P0DTC6-1", "Evasion of Type I Interferon by SARS-CoV-2.", "Cell Rep.", "2020", "Wang H., Zhang X., Xie X., Cao Z., Xia H., Chen J.Y., Shi P.Y., Rajsbaum R., Menachery V.D.", "protein_xref_pubmed", "32979938", "protein_xref_uniprotkb", "P0DTC6" ], [ "P0DTC5-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC5" ], [ "P0DTC4-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC4" ], [ "P0DTC4-1", "SARS-CoV-2 envelope protein topology in eukaryotic membranes.", "Open Biol.", "2020", "Martinez-Gil L., Mingarro I., Acosta-Caceres J.M., Duart G., Garcia-Murria M.J., Grau B.", "protein_xref_pubmed", "32898469", "protein_xref_uniprotkb", "P0DTC4" ], [ "P0DTC3-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC3" ], [ "P0DTC3-1", "beta-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway.", "Cell", "2020", "Hsu V.W., Fisher M., Perlman S., Qiu Q., Ghosh S., Pak E., Altan-Bonnet N., Fehr A.R., Kehrl J., Whittaker G.R., Achar S.R., Altan-Bonnet G., Bleck C., Dellibovi-Ragheb T.A., Kerviel A., Straus M.R., Takvorian P.M., de Haan C.A.M.", "protein_xref_pubmed", "33157038", "protein_xref_uniprotkb", "P0DTC3" ], [ "P0DTC2-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.", "Science", "2020", "Wang N., McLellan J.S., Graham B.S., Hsieh C.L., Abiona O., Corbett K.S., Goldsmith J.A., Wrapp D.", "protein_xref_pubmed", "32075877", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor.", "Cell", "2020", "Poehlmann S., Schroeder S., Drosten C., Hoffmann M., Herrler G., Erichsen S., Herrler T., Kleine-Weber H., Krueger N., Mueller M.A., Nitsche A., Schiergens T.S., Wu N.H.", "protein_xref_pubmed", "32142651", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein.", "Cell", "2020", "Park Y.J., McGuire A.T., Tortorici M.A., Veesler D., Wall A., Walls A.C.", "protein_xref_pubmed", "32155444", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV.", "Nat. Commun.", "2020", "Chen J., Chen X., Li P., Liu Y., Wang J., Chen T., Hu J., Hu K., Guo L., Jin Q., Lei X., Guo R., Qian Z., Ren L., Ou X., Xiang Z., Mi D., Mu Z.", "protein_xref_pubmed", "32221306", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.", "Cell", "2020", "Tang H., Parker M.D., Whelan S.P., Evans C.M., Yoon H., Saphire E.O., Abfalterer W., Bhattacharya T., Fischer W.M., Foley B., Freeman T.M., Giorgi E.E., Gnanakaran S., Hastie K.M., Hengartner N., Korber B., LaBranche C.C., McDanal C., Montefiori D.C., Moon-Walker A., Partridge D.G., Perez L.G., Theiler J., de Silva T.I.", "protein_xref_pubmed", "32697968", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide.", "Sci. Rep.", "2020", "Bundalovic-Torma C., Eshaghi A., Grana-Miraglia L., Groves H.E., Gubbay J.B., Gutierrez J.M., Guttman D.S., Isabel M.R., Isabel S., Patel S.N., Poutanen S.M., Poutanen T.", "protein_xref_pubmed", "32820179", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.", "Sci. Rep.", "2020", "Ito K., Montgomery D., Woods R.J., Grant O.C.", "protein_xref_pubmed", "32929138", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.", "Cell", "2020", "Huang W., Li X., Liu H., Liu J., Liu S., Wang Y., Wu J., Zhang L., Zhang Q., Li Q., Lu Q., Wang M., Zhao C., Li X.', Sun Q., Nie J., Hao H., Qin H., Nie L., Zhang L.'", "protein_xref_pubmed", "32730807", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy.", "Science", "2020", "Chen S., Han G., He L., Li J., Li Y., Wang H., Wang X., Wang Y., Yang X., Zhao G., Zhao Z., Zhou X., Zhou Y., Chen Q., Guo Y., He Y., Gu H., Jiang S., Cui Y., Fan H., Li Y.', Yang G., Sun S., Sheng X., Li X.F., Teng Y., Yang X.', Deng Y.Q., Geng S., Luo D.Y., Qin C.F., Zhang N.N.", "protein_xref_pubmed", "32732280", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo.", "Science", "2020", "Graham R., Nakajima N., Suzuki T., Takahashi K., Chiba S., Okuda K., Schaefer A., Kuroda M., Boucher R.C., Kawaoka Y., Randell S.H., Gralinski L.E., Hou Y.J., Baric R.S., Bartelt L., Dinnon K.H. III, Edwards C.E., Ehre C., Halfmann P., Lee R.E., Leist S.R., Margolis D.M., Markmann A.J., Mascenik T.M., Tse L.V., de Silva A.", "protein_xref_pubmed", "33184236", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC2-1", "Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2.", "PLoS Pathog.", "2021", "Zhang L., Choe H., Farzan M., Mou H., Ojha A., Ou T.", "protein_xref_pubmed", "33465165", "protein_xref_uniprotkb", "P0DTC2" ], [ "P0DTC1-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.", "Cell", "2020", "Gao Y., Wang H., Wang Q., Wu J., Xu W., Yang H., Yang X., Zhu Y., Ge J., Huang Y., Liu Z., Yan L., Guddat L.W., Liu Q., Liu F., Rao Z., Zhu C., Gao H., Ji W., Sun Q., Fang X., Jiang B., Lou Z., Gong P., Mu A., Yang X.'", "protein_xref_pubmed", "32526208", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "Activation and evasion of type I interferon responses by SARS-CoV-2.", "Nat. Commun.", "2020", "Li L., Wang C., Wang J., Wang W., Wang Y., Zhao Z., Xiao X., Zhou Z., Guo F., Lei X., Dong X., Tian Z., Ren L., Ma R., Xiang Z.", "protein_xref_pubmed", "32733001", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.", "Nat. Struct. Mol. Biol.", "2020", "Ban N., Thiel V., Schubert K., Echeverria B., Gurzeler L.A., Jomaa A., Karousis E.D., Leibundgut M., Muehlemann O., Scaiola A.", "protein_xref_pubmed", "32908316", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "Evasion of Type I Interferon by SARS-CoV-2.", "Cell Rep.", "2020", "Wang H., Zhang X., Xie X., Cao Z., Xia H., Chen J.Y., Shi P.Y., Rajsbaum R., Menachery V.D.", "protein_xref_pubmed", "32979938", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses.", "Cell", "2020", "Lin A.E., Majumdar D., Guttman M., Chen L.M., Chow A., Banerjee A.K., Bhat P., Blanco M.R., Botten J.W., Bruce E.A., De Lorenzo G., Goldfarb D., Honson D.D., Loney C., Miller Z.D., Ollikainen N., Quinodoz S.A., Rihn S.J., Schmidt M.M., Stewart D.G., Thai J., Voorhees R.M.", "protein_xref_pubmed", "33080218", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTC1-1", "ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity.", "Nat. Microbiol.", "2021", "Liu G., Lee J.H., Chiang C., Gack M.U., Wies E., Chiang J.J., Parker Z.M., Acharya D., Davis-Gardner M.E., Riedl W., van Gent M.", "protein_xref_pubmed", "33727702", "protein_xref_uniprotkb", "P0DTC1" ], [ "P0DTD8-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTD8" ], [ "P0DTG0-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTG0" ], [ "P0DTG0-1", "Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.", "Emerg. Microbes Infect.", "2020", "Zhu Z., Yuan S., Kok K.H., Chu H., Yuen K.Y., Chan J.F., To K.K.", "protein_xref_pubmed", "31987001", "protein_xref_uniprotkb", "P0DTG0" ], [ "P0DTF1-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTF1" ], [ "P0DTF1-1", "Characterization of accessory genes in coronavirus genomes.", "Virol. J.", "2020", "Poch O., Mayer C., Thompson J.D., Michel C.J.", "protein_xref_pubmed", "32854725", "protein_xref_uniprotkb", "P0DTF1" ], [ "P0DTF1-1", "SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant.", "Cell Rep.", "2020", "Nakagawa S., Sato K., Fukushi M., Koyanagi Y., Kimura I., Konno Y., Irie T., Gifford R.J., Sauter D., Uriu K.", "protein_xref_pubmed", "32941788", "protein_xref_uniprotkb", "P0DTF1" ], [ "P0DTC9-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC9" ], [ "P0DTC9-1", "Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites.", "Acta Pharmacol. Sin.", "2020", "Chen S., Chen X., Zhang C., Zhang L., Chen Q., Zhou Z., Yan Y., Hong Z., Yang M., He S., Kang S., Huang Z., Shan H., Zhou Z.'", "protein_xref_pubmed", "32363136", "protein_xref_uniprotkb", "P0DTC9" ], [ "P0DTC8-1", "A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster.", "Lancet", "2020", "Liu J., Yang J., Chen H., Yuan S., Chan W.M., Cai J.P., Kok K.H., Chu H., Yip C.C., Chan K.H., Yuen K.Y., Chan J.F., Cheng V.C., Hui C.K., Ip J.D., Lo S.K., Poon R.W., Poon V.K., To K.K., Tsoi H.W., Xing F.", "protein_xref_pubmed", "31986261", "protein_xref_uniprotkb", "P0DTC8" ], [ "P0DTC8-1", "A new coronavirus associated with human respiratory disease in China.", "Nature", "2020", "Hu Y., Liu Y., Wang W., Zhao S., Xu L., Wu F., Yu B., Zhang Y.-L., Zhang Y.-Z., Zhang Y.L., Tian J.H., Zheng J.J., Zhang Y.Z., Chen Y.M., Chen Y.-M., Wang Q.M., Dai F.-H., Holmes E.C., Pei Y.-Y., Song Z.-G., Tao Z.-W., Tian J.-H., Wang Q.-M., Yuan M.-L., Zheng J.-J., Dai F.H., Pei Y.Y., Song Z.G., Tao Z.W., Yuan M.L.", "protein_xref_pubmed", "32015508", "protein_xref_uniprotkb", "P0DTC8" ], [ "P0DTC8-1", "Characterization of accessory genes in coronavirus genomes.", "Virol. J.", "2020", "Poch O., Mayer C., Thompson J.D., Michel C.J.", "protein_xref_pubmed", "32854725", "protein_xref_uniprotkb", "P0DTC8" ], [ "P0DTC8-1", "Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission.", "Infect. Genet. Evol.", "2020", "Das S., Biswas S., Laha S., Chakraborty J., Chatterjee R., Manna S.K.", "protein_xref_pubmed", "32615316", "protein_xref_uniprotkb", "P0DTC8" ], [ "P0DTC8-1", "Title: ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway.", "IScience", "2021", "Fu B., Li Z., Liu H., Wang P., Wang X., Wang Y., Wu H., Xu S., Zhang H., Zhang J., Zhang S., Zhao Q., Xiong Y., Lin X., Yin S., Xue W., Nian W., Xing N.", "protein_xref_pubmed", "33723527", "protein_xref_uniprotkb", "P0DTC8" ] ] }, "readme": "Name\n - SARS-CoV2 Protein Citations (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-19T11:32:35.963024\n\nModified on\n - 2020-04-19T11:33:03.867613\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein Citations dataset contains publication information for sarscov2 [taxid:2697049] UniProtKB accessions that includes PMID, journal name, date and author and title. The dataset is derived from 2020-01 UniProt release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-sars-cov-2.nt\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_masterlist.csv\n Output Subdomain\n Name: sarscov2_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_citations_uniprotkb.csv\n Name: sarscov2_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/sarscov2_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_citations_uniprotkb.csv" }