Skip to content

Commit 75dc97a

Browse files
committed
Documentation updates
1 parent 9af327d commit 75dc97a

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

57 files changed

+210
-210
lines changed

alhazen/tools/tiab_mapping_tool.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@
4848
# %% ../../nbs/tools/26_tiab_mapping_tool.ipynb 4
4949
class TitleAbstractMappingToolSchema(BaseModel):
5050
collection_id: str = Field(description="the id of the collection being analyzed.")
51-
repeat_run: Optional[bool] = Field(description="Whether or not to repeat the classification task if it has been performed before. Defaults to False.")
51+
repeat_run: Optional[bool] = Field(description="Whether or not to repeat the mapping task if it has been performed before. Defaults to False.")
5252
run_label: Optional[str] = Field(description="This is a label that will be used to identify the run of the tool in the database. Defaults to 'dev'")
5353

5454
class BaseTitleAbstractMappingTool(BaseTool, AlhazenToolMixin):

docs/91_ssl_hackfix.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -274,19 +274,19 @@
274274
<li class="sidebar-item">
275275
<div class="sidebar-item-container">
276276
<a href="./tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
277-
<span class="menu-text">Document Classifier Tool</span></a>
277+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
278278
</div>
279279
</li>
280280
<li class="sidebar-item">
281281
<div class="sidebar-item-container">
282282
<a href="./tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
283-
<span class="menu-text">Document Classifier Tool</span></a>
283+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
284284
</div>
285285
</li>
286286
<li class="sidebar-item">
287287
<div class="sidebar-item-container">
288288
<a href="./tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
289-
<span class="menu-text">Document Classifier Tool</span></a>
289+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
290290
</div>
291291
</li>
292292
</ul>

docs/agents/agent.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -243,19 +243,19 @@
243243
<li class="sidebar-item">
244244
<div class="sidebar-item-container">
245245
<a href="../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
246-
<span class="menu-text">Document Classifier Tool</span></a>
246+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
247247
</div>
248248
</li>
249249
<li class="sidebar-item">
250250
<div class="sidebar-item-container">
251251
<a href="../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
252-
<span class="menu-text">Document Classifier Tool</span></a>
252+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
253253
</div>
254254
</li>
255255
<li class="sidebar-item">
256256
<div class="sidebar-item-container">
257257
<a href="../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
258-
<span class="menu-text">Document Classifier Tool</span></a>
258+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
259259
</div>
260260
</li>
261261
</ul>

docs/agents/index.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -302,19 +302,19 @@
302302
<li class="sidebar-item">
303303
<div class="sidebar-item-container">
304304
<a href="../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
305-
<span class="menu-text">Document Classifier Tool</span></a>
305+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
306306
</div>
307307
</li>
308308
<li class="sidebar-item">
309309
<div class="sidebar-item-container">
310310
<a href="../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
311-
<span class="menu-text">Document Classifier Tool</span></a>
311+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
312312
</div>
313313
</li>
314314
<li class="sidebar-item">
315315
<div class="sidebar-item-container">
316316
<a href="../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
317-
<span class="menu-text">Document Classifier Tool</span></a>
317+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
318318
</div>
319319
</li>
320320
</ul>

docs/aliases.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -243,19 +243,19 @@
243243
<li class="sidebar-item">
244244
<div class="sidebar-item-container">
245245
<a href="./tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
246-
<span class="menu-text">Document Classifier Tool</span></a>
246+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
247247
</div>
248248
</li>
249249
<li class="sidebar-item">
250250
<div class="sidebar-item-container">
251251
<a href="./tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
252-
<span class="menu-text">Document Classifier Tool</span></a>
252+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
253253
</div>
254254
</li>
255255
<li class="sidebar-item">
256256
<div class="sidebar-item-container">
257257
<a href="./tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
258-
<span class="menu-text">Document Classifier Tool</span></a>
258+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
259259
</div>
260260
</li>
261261
</ul>

docs/cookbook/admin/postgresql_fixes.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/general_workbook.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/key_opinion_leaders/african_microscopy.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/key_opinion_leaders/index.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -302,19 +302,19 @@
302302
<li class="sidebar-item">
303303
<div class="sidebar-item-container">
304304
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
305-
<span class="menu-text">Document Classifier Tool</span></a>
305+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
306306
</div>
307307
</li>
308308
<li class="sidebar-item">
309309
<div class="sidebar-item-container">
310310
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
311-
<span class="menu-text">Document Classifier Tool</span></a>
311+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
312312
</div>
313313
</li>
314314
<li class="sidebar-item">
315315
<div class="sidebar-item-container">
316316
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
317-
<span class="menu-text">Document Classifier Tool</span></a>
317+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
318318
</div>
319319
</li>
320320
</ul>

docs/cookbook/personal_use/machine_learning_in_biology copy.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/question_answering/cellbiology.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/question_answering/index.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -302,19 +302,19 @@
302302
<li class="sidebar-item">
303303
<div class="sidebar-item-container">
304304
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
305-
<span class="menu-text">Document Classifier Tool</span></a>
305+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
306306
</div>
307307
</li>
308308
<li class="sidebar-item">
309309
<div class="sidebar-item-container">
310310
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
311-
<span class="menu-text">Document Classifier Tool</span></a>
311+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
312312
</div>
313313
</li>
314314
<li class="sidebar-item">
315315
<div class="sidebar-item-container">
316316
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
317-
<span class="menu-text">Document Classifier Tool</span></a>
317+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
318318
</div>
319319
</li>
320320
</ul>

docs/cookbook/question_answering/virtualcell_corepapers.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/single_doc_extraction/cellxgene_datasets.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/single_doc_extraction/cryoet.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/single_doc_extraction/index.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -302,19 +302,19 @@
302302
<li class="sidebar-item">
303303
<div class="sidebar-item-container">
304304
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
305-
<span class="menu-text">Document Classifier Tool</span></a>
305+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
306306
</div>
307307
</li>
308308
<li class="sidebar-item">
309309
<div class="sidebar-item-container">
310310
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
311-
<span class="menu-text">Document Classifier Tool</span></a>
311+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
312312
</div>
313313
</li>
314314
<li class="sidebar-item">
315315
<div class="sidebar-item-container">
316316
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
317-
<span class="menu-text">Document Classifier Tool</span></a>
317+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
318318
</div>
319319
</li>
320320
</ul>

docs/cookbook/single_doc_extraction/ncats_natural_history_studies.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

docs/cookbook/single_doc_extraction/rnaquarium.html

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -277,19 +277,19 @@
277277
<li class="sidebar-item">
278278
<div class="sidebar-item-container">
279279
<a href="../../tools/tiab_clasifier_tool.html" class="sidebar-item-text sidebar-link">
280-
<span class="menu-text">Document Classifier Tool</span></a>
280+
<span class="menu-text">Title / Abstract Classifier Tool</span></a>
281281
</div>
282282
</li>
283283
<li class="sidebar-item">
284284
<div class="sidebar-item-container">
285285
<a href="../../tools/tiab_mapping_tool.html" class="sidebar-item-text sidebar-link">
286-
<span class="menu-text">Document Classifier Tool</span></a>
286+
<span class="menu-text">Title / Abstract Mapping Tool</span></a>
287287
</div>
288288
</li>
289289
<li class="sidebar-item">
290290
<div class="sidebar-item-container">
291291
<a href="../../tools/tiab_extraction_tool.html" class="sidebar-item-text sidebar-link">
292-
<span class="menu-text">Document Classifier Tool</span></a>
292+
<span class="menu-text">Title / Abstract Extraction Tool</span></a>
293293
</div>
294294
</li>
295295
</ul>

0 commit comments

Comments
 (0)