PMC:7253482 / 34340-35483
Annnotations
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
1015 | 185-193 | Species | denotes | SARS-CoV | Tax:694009 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T103 | 185-193 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T104 | 185-189 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T243 | 577-578 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T244 | 646-647 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T245 | 648-650 | http://purl.obolibrary.org/obo/CLO_0037127 | denotes | K2 |
T246 | 886-889 | http://purl.obolibrary.org/obo/CLO_0001320 | denotes | 381 |
T247 | 886-889 | http://purl.obolibrary.org/obo/CLO_0001321 | denotes | 381 |
T248 | 925-926 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T249 | 977-978 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T365 | 5-7 | Chemical | denotes | EM | http://purl.obolibrary.org/obo/CHEBI_73507 |
T366 | 61-63 | Chemical | denotes | EM | http://purl.obolibrary.org/obo/CHEBI_73507 |
T367 | 583-588 | Chemical | denotes | Titan | http://purl.obolibrary.org/obo/CHEBI_33341 |
LitCovid-sample-MedDRA
Id | Subject | Object | Predicate | Lexical cue | meddra_id |
---|---|---|---|---|---|
T14 | 732-740 | http://purl.bioontology.org/ontology/MEDDRA/10022891 | denotes | weighted | http://purl.bioontology.org/ontology/MEDDRA/10047890 |
LitCovid-sample-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T254 | 583-588 | Chemical | denotes | Titan | http://purl.obolibrary.org/obo/CHEBI_33341 |
LitCovid-sample-PD-NCBITaxon
Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
---|---|---|---|---|---|
T215 | 185-193 | Species | denotes | SARS-CoV | NCBItxid:694009 |
T216 | 185-189 | Species | denotes | SARS | NCBItxid:694009 |
T217 | 603-609 | Species | denotes | Fisher | NCBItxid:76720 |
LitCovid-sample-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T206 | 0-39 | Sentence | denotes | Cryo-EM data analysis and visualization |
T207 | 40-171 | Sentence | denotes | Single-particle cryo-EM data analysis of BG505 SOSIP.664 in complex with RM20A3 Fab was reproduced directly from Berndsen et al.51. |
T208 | 172-398 | Sentence | denotes | Data for the SARS-CoV S 2P ectodomain was previously published52 and the final particle stack and alignment parameters from the published reconstruction were used for 3D variability analysis in the SPARX software package76,77. |
T209 | 399-533 | Sentence | denotes | All metadata for these reconstructions along with raw data images and FSC resolution curves can be found in the original publications. |
T210 | 534-691 | Sentence | denotes | In summary, both datasets were acquired on a FEI Titan Krios (Thermo Fisher) operating at 300 KeV equipped with a K2 Summit Direct Electron Detector (Gatan). |
T211 | 692-804 | Sentence | denotes | Movie micrographs were aligned and dose weighted with MotionCor278 and CTF estimation was performed with Gctf79. |
T212 | 805-890 | Sentence | denotes | Single-particle data processing was performed using CryoSparc v.280 and Relion v.381. |
T213 | 891-976 | Sentence | denotes | Maps were low-pass filtered using a Gaussian kernel and visualized in UCSF chimera82. |
T214 | 977-1143 | Sentence | denotes | A detailed description of the auto-thresholding method used to set the isosurface value for visualisation of low-pass filtered maps can be found in Berndsen et al.51. |
LitCovid-sample-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T98 | 185-193 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T99 | 185-189 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-sample-Pubtator
Id | Subject | Object | Predicate | Lexical cue | pubann:denotes |
---|---|---|---|---|---|
1015 | 185-193 | Species | denotes | SARS-CoV | Tax:694009 |
LitCovid-sample-UniProt
Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
---|---|---|---|---|---|
T6450 | 763-766 | Protein | denotes | CTF | https://www.uniprot.org/uniprot/Q9Y6R8|https://www.uniprot.org/uniprot/Q9UPK1|https://www.uniprot.org/uniprot/Q9UPK0|https://www.uniprot.org/uniprot/Q9UPJ9|https://www.uniprot.org/uniprot/Q9UPJ3|https://www.uniprot.org/uniprot/Q9UPH1|https://www.uniprot.org/uniprot/Q9R1G5|https://www.uniprot.org/uniprot/Q9R1G4|https://www.uniprot.org/uniprot/Q9R1G3|https://www.uniprot.org/uniprot/Q9R1G2|https://www.uniprot.org/uniprot/Q9P2A9|https://www.uniprot.org/uniprot/Q9H3X9|https://www.uniprot.org/uniprot/Q99MA8|https://www.uniprot.org/uniprot/Q99MA7|https://www.uniprot.org/uniprot/Q99MA6|https://www.uniprot.org/uniprot/Q99MA5|https://www.uniprot.org/uniprot/Q99MA4|https://www.uniprot.org/uniprot/Q99MA3|https://www.uniprot.org/uniprot/Q99L78|https://www.uniprot.org/uniprot/Q96J45|https://www.uniprot.org/uniprot/Q90932|https://www.uniprot.org/uniprot/Q8VBT5|https://www.uniprot.org/uniprot/Q8TA97|https://www.uniprot.org/uniprot/Q6ZNF9|https://www.uniprot.org/uniprot/Q64192|https://www.uniprot.org/uniprot/Q63HM5|https://www.uniprot.org/uniprot/Q63782|https://www.uniprot.org/uniprot/Q61960|https://www.uniprot.org/uniprot/Q5VW29|https://www.uniprot.org/uniprot/Q5U094|https://www.uniprot.org/uniprot/Q54A99|https://www.uniprot.org/uniprot/Q3UUZ2|https://www.uniprot.org/uniprot/Q3U2I9|https://www.uniprot.org/uniprot/Q14938|https://www.uniprot.org/uniprot/Q14932|https://www.uniprot.org/uniprot/Q13052|https://www.uniprot.org/uniprot/Q13050|https://www.uniprot.org/uniprot/Q12859|https://www.uniprot.org/uniprot/Q12858|https://www.uniprot.org/uniprot/Q12857|https://www.uniprot.org/uniprot/Q0VG09|https://www.uniprot.org/uniprot/Q02780|https://www.uniprot.org/uniprot/P97863|https://www.uniprot.org/uniprot/P70258|https://www.uniprot.org/uniprot/P70257|https://www.uniprot.org/uniprot/P70256|https://www.uniprot.org/uniprot/P70255|https://www.uniprot.org/uniprot/P70254|https://www.uniprot.org/uniprot/P70253|https://www.uniprot.org/uniprot/P70252|https://www.uniprot.org/uniprot/P70251|https://www.uniprot.org/uniprot/P70250|https://www.uniprot.org/uniprot/P21999|https://www.uniprot.org/uniprot/P17926|https://www.uniprot.org/uniprot/P17925|https://www.uniprot.org/uniprot/P17924|https://www.uniprot.org/uniprot/P17923|https://www.uniprot.org/uniprot/P14057|https://www.uniprot.org/uniprot/P13623|https://www.uniprot.org/uniprot/P13622|https://www.uniprot.org/uniprot/P09414|https://www.uniprot.org/uniprot/P08652|https://www.uniprot.org/uniprot/P08651|https://www.uniprot.org/uniprot/O60413|https://www.uniprot.org/uniprot/O09072|https://www.uniprot.org/uniprot/O08519|https://www.uniprot.org/uniprot/O00712|https://www.uniprot.org/uniprot/O00166|https://www.uniprot.org/uniprot/K7EMU1|https://www.uniprot.org/uniprot/H7BYE8|https://www.uniprot.org/uniprot/G3V1P1|https://www.uniprot.org/uniprot/F8W8W3|https://www.uniprot.org/uniprot/F5H0R0|https://www.uniprot.org/uniprot/B7Z9C3|https://www.uniprot.org/uniprot/B7Z4U5|https://www.uniprot.org/uniprot/B4DS53|https://www.uniprot.org/uniprot/B4DRJ3|https://www.uniprot.org/uniprot/B4DM25|https://www.uniprot.org/uniprot/A8K1H0 |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T206 | 0-39 | Sentence | denotes | Cryo-EM data analysis and visualization |
T207 | 40-171 | Sentence | denotes | Single-particle cryo-EM data analysis of BG505 SOSIP.664 in complex with RM20A3 Fab was reproduced directly from Berndsen et al.51. |
T208 | 172-398 | Sentence | denotes | Data for the SARS-CoV S 2P ectodomain was previously published52 and the final particle stack and alignment parameters from the published reconstruction were used for 3D variability analysis in the SPARX software package76,77. |
T209 | 399-533 | Sentence | denotes | All metadata for these reconstructions along with raw data images and FSC resolution curves can be found in the original publications. |
T210 | 534-691 | Sentence | denotes | In summary, both datasets were acquired on a FEI Titan Krios (Thermo Fisher) operating at 300 KeV equipped with a K2 Summit Direct Electron Detector (Gatan). |
T211 | 692-804 | Sentence | denotes | Movie micrographs were aligned and dose weighted with MotionCor278 and CTF estimation was performed with Gctf79. |
T212 | 805-890 | Sentence | denotes | Single-particle data processing was performed using CryoSparc v.280 and Relion v.381. |
T213 | 891-976 | Sentence | denotes | Maps were low-pass filtered using a Gaussian kernel and visualized in UCSF chimera82. |
T214 | 977-1143 | Sentence | denotes | A detailed description of the auto-thresholding method used to set the isosurface value for visualisation of low-pass filtered maps can be found in Berndsen et al.51. |
LitCovid-sample-Glycan
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T50 | 399-402 | https://glytoucan.org/Structures/Glycans/G05518TD | denotes | All |