PMC:7473770 / 40979-42287
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T241 | 164-170 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T242 | 352-363 | Body_part | denotes | macrophages | http://purl.org/sig/ont/fma/fma63261 |
| T243 | 376-382 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T244 | 396-419 | Body_part | denotes | connected to the tissue | http://purl.org/sig/ont/fma/fma9640 |
| T245 | 413-419 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T246 | 459-462 | Body_part | denotes | map | http://purl.org/sig/ont/fma/fma67847 |
| T247 | 519-531 | Body_part | denotes | compartments | http://purl.org/sig/ont/fma/fma76577 |
| T248 | 566-572 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T249 | 780-786 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T250 | 798-804 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T251 | 859-865 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T252 | 905-911 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T253 | 1221-1227 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T254 | 1254-1265 | Body_part | denotes | compartment | http://purl.org/sig/ont/fma/fma76577 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T240 | 164-170 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T241 | 376-382 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T242 | 413-419 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T243 | 566-572 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T244 | 780-786 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T245 | 798-804 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T246 | 859-865 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T247 | 905-911 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T248 | 1221-1227 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T391 | 144-149 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 2 × 2 |
| T392 | 396-419 | http://purl.obolibrary.org/obo/UBERON_0002384 | denotes | connected to the tissue |
| T393 | 396-419 | http://www.ebi.ac.uk/efo/EFO_0000952 | denotes | connected to the tissue |
| T394 | 924-925 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T395 | 1072-1073 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T396 | 1099-1101 | http://purl.obolibrary.org/obo/CL_0000453 | denotes | Lc |
| T397 | 1133-1134 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T46 | 230-242 | http://purl.obolibrary.org/obo/GO_0035282 | denotes | segmentation |
| T47 | 690-702 | http://purl.obolibrary.org/obo/GO_0035282 | denotes | segmentation |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T319 | 0-101 | Sentence | denotes | For each patient the stitched overview scans were analyzed with regard to structural characteristics. |
| T320 | 102-324 | Sentence | denotes | The 3D-reconstructions were first binned (2 × 2 × 2), and the tissue was then segmented from the surrounding paraffin using the segmentation software Ilastik (Berg et al., 2019), which was then further refined with MATLAB. |
| T321 | 325-463 | Sentence | denotes | In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. |
| T322 | 464-579 | Sentence | denotes | Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. |
| T323 | 580-675 | Sentence | denotes | Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. |
| T324 | 676-793 | Sentence | denotes | Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. |
| T325 | 794-866 | Sentence | denotes | The tissue volume V is given by the sum of all voxels containing tissue. |
| T326 | 867-957 | Sentence | denotes | The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. |
| T327 | 958-1063 | Sentence | denotes | From this information we calculated the specific surface(2) SV=SA/Vwith SA/V surface area volume -ratio. |
| T328 | 1064-1172 | Sentence | denotes | Further a characteristic length(3) Lc=V/SA⋅vxwith vx edge length of a voxel was determined for each sample. |
| T329 | 1173-1308 | Sentence | denotes | Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32815517-31570887-26997871 | 274-278 | 31570887 | denotes | 2019 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32815517-31570887-26997871 | 274-278 | 31570887 | denotes | 2019 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 326 | 9-16 | Species | denotes | patient | Tax:9606 |
| 327 | 211-219 | Chemical | denotes | paraffin | MESH:D010232 |
| 328 | 490-498 | Chemical | denotes | paraffin | MESH:D010232 |
| 329 | 615-623 | Chemical | denotes | paraffin | MESH:D010232 |
| 330 | 749-755 | Chemical | denotes | oxygen | MESH:D010100 |
| 331 | 884-886 | Chemical | denotes | SA | MESH:C012546 |