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| 1 | -#Automatic Extraction of "Growth Conditions (GC)" from the "Gene Expression Omnibus (GEO)". | 1 | +# "Automatic Extraction of Growth Conditions (GC) from the Gene Expression Omnibus (GEO)". |
| 2 | -Proyecto para extraer de manera automática las condiciones de crecimiento de todas las enterobacterias de la GEO con ayuda de "Conditional Random Fields (CRFs)". | 2 | +Project to extract in an automatic way, the growth conditions of all enterobacteria within the GEO using "Conditional Random Fields " (CRFs). |
| 3 | 3 | ||
| 4 | +## Prerequisites | ||
| 5 | +### Programming languages | ||
| 6 | + - Python (version 2.7, version 3) | ||
| 7 | + - Bash | ||
| 8 | + | ||
| 9 | +## Folder content | ||
| 10 | +**CRF** | ||
| 11 | + - bin | ||
| 12 | + 1. label-split_training_test_v1.py | ||
| 13 | + 2. params.py | ||
| 14 | + 3. training_validation_v3.py | ||
| 15 | + - check | ||
| 16 | + 1. sentences-405-order-rep.txt | ||
| 17 | + - data-sets | ||
| 18 | + 1. test-data-set-30.txt | ||
| 19 | + 2. training-data-set-70.txt | ||
| 20 | + - models | ||
| 21 | + 1. training-data-set-70.fStopWords_False.fSymbols_False.mod | ||
| 22 | + - reports | ||
| 23 | + 1. report_training-data-set-70.fStopWords_False.fSymbols_False.txt | ||
| 24 | + 2. y_pred_training-data-set-70.fStopWords_False.fSymbols_False.txt | ||
| 25 | + 3. y_test_training-data-set-70.fStopWords_False.fSymbols_False.txt | ||
| 26 | + | ||
| 27 | +**CoreNLP** | ||
| 28 | + - bin | ||
| 29 | + 1. get-raw-sentences.sh | ||
| 30 | + 2. single_run.sh | ||
| 31 | + - input | ||
| 32 | + 1. raw-metadata-senteneces.txt | ||
| 33 | + - output | ||
| 34 | + 1. raw-metadata-senteneces.txt.conll | ||
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