UCDenver-ccp Cartoomics issues

UCDenver-ccp / Cartoomics

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read me updates

#128 bsantan opened 6 months ago
0
Literature evaluation updates

#127 bsantan opened 6 months ago
0
Results 2024 05 28

#126 bsantan opened 6 months ago
0
Update creating_subgraph_from_KG.py

#125 bsantan closed 6 months ago
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More ontologies

#124 bsantan closed 6 months ago
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ablations to gitignore

#123 bsantan closed 6 months ago
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information content results

#122 bsantan closed 6 months ago
0
Information content filtering

#121 bsantan closed 6 months ago
1
Merge pull request #119 from UCDenver-ccp/main

#120 bsantan closed 7 months ago
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pull all annotations in

#119 bsantan closed 7 months ago
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added partial and abstract annotations

#118 bsantan closed 7 months ago
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remove extra networkx_graph variable, remove mem management code

#117 bsantan closed 7 months ago
0
Full text evaluation

#116 bsantan closed 7 months ago
2
New node exclusion

#115 bsantan closed 7 months ago
4
Excluding broad nodes

#114 bsantan closed 7 months ago
1
Literature comparison heatmap

#113 lagillenwater closed 7 months ago
4
Full text files for concept annotations.

#112 bsantan closed 7 months ago
0
fix pdp by passing shortest path nodes when already calculated

#111 bsantan closed 8 months ago
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add CLO to ontology labels

#110 bsantan closed 8 months ago
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manual results for WP5372 ner

#109 bsantan closed 8 months ago
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WP5372 output

#108 bsantan closed 8 months ago
0
2024 03 23 alpine results

#107 bsantan closed 8 months ago
0
Merge pull request #105 from UCDenver-ccp/2024_03_23_alpine_results

#106 bsantan closed 8 months ago
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All results, not WP4541 because not complete.

#105 bsantan closed 8 months ago
0
Ner manual results

#104 bsantan closed 8 months ago
0
Fix shortest path calling igraph and networx implementation in cs

#103 bsantan closed 8 months ago
0
Comparing branches

#102 bsantan closed 7 months ago
1
ingest other ner results for literature comparison

#101 bsantan closed 8 months ago
0
script to output visualizations, update evaluation to use node_IDs, streamline idf and literature evals to use node_IDs

#100 bsantan closed 8 months ago
0
35 node similarity metric

#99 bsantan closed 8 months ago
0
Add networkx changes

#98 bsantan closed 8 months ago
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Networkx shortest path

#97 lagillenwater closed 8 months ago
0
Untested addition of S_ID, P_ID, and O_ID to subgraph file for kg-covid.

#96 bsantan closed 8 months ago
0
Support for literature comparison

#95 bsantan closed 8 months ago
2
Alpine tests

#94 bsantan closed 9 months ago
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visualize cosine similarity scores to wikipathways guiding terms

#93 bsantan opened 9 months ago
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report random cosine similarity metrics via permutation of intermediate nodes

#92 bsantan opened 9 months ago
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report average cosine similarity metric for all nodes within a subgraph to a guiding term

#91 bsantan opened 9 months ago
0
select guiding term for each wikipathways diagram based on paper

#90 bsantan opened 9 months ago
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visualize evaluation metrics for ontology types of wiki pathways subgraphs

#89 bsantan opened 9 months ago
0
ReadMe updates about running with Wikipathways diagrams.

#88 bsantan closed 9 months ago
0
Modify cosine similarity based graph extraction to take into account guiding terms

#87 bsantan opened 9 months ago
0
Parameterize the input format (i.e., pre-defined graph or list of entities)

#86 bsantan opened 9 months ago
0
Define specific versions of packages in environment.yml

#85 bsantan opened 9 months ago
0
Select 1 node when there is an exact match for duplicate node labels

#84 bsantan opened 9 months ago
0
Handle placeholder nodes in wiki pathways diagrams

#83 bsantan opened 9 months ago
0
Separate indexing step and subgraph generation step in wikipathways pipeline

#82 bsantan opened 9 months ago
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Keep track of nodes that do not have a URI from Wikipathways metadata or node normalizer

#81 bsantan opened 9 months ago
0
78 use wikipathways node metadata

#80 bsantan closed 9 months ago
6
Perform node matching using node normalizer API

#79 bsantan opened 9 months ago
0