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Carlos-Francisco Méndez-Cruz
/
automatic-extraction-growth-conditions
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Authored by
Kevin Meza Landeros
2019-07-09 17:10:01 -0500
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# "Automatic Extraction of Growth Conditions (GC) from the Gene Expression Omnibus (GEO)".
Project to extract in an automatic way
,
the growth conditions of all enterobacteria within the GEO using "Conditional Random Fields " (CRFs).
# "Automatic Extraction of Growth Conditions (GC
s
) from the Gene Expression Omnibus (GEO)".
Project to extract in an automatic way the growth conditions of all enterobacteria within the GEO using "Conditional Random Fields " (CRFs).
## Prerequisites
### Programming languages
-
Python (version 2.7, version 3)
-
Python (version 2.7, version 3
.7
)
-
Bash
## Folder content
...
...
@@ -26,9 +26,19 @@ Project to extract in an automatic way, the growth conditions of all enterobacte
**CoreNLP**
-
bin
1.
get-raw-sentences.sh
2.
single_run.sh
1.
get-raw-sentences.sh
_Script that
**extracts the GCs**
from the file: "tagged-xml-data" and adds the phrase: "PGCGROWTHCONDITIONS" to all lines._
2.
single_run.sh
_Script that
**runs**
th script: "corenlp.sh" with the desired parameters._
-
input
1.
raw-metadata-senteneces.txt
1.
raw-metadata-senteneces.txt
_Resulting file from "get-raw-sentences.sh".
**Contains all the GCs.**
_
-
output
1.
raw-metadata-senteneces.txt.conll
\ No newline at end of file
1.
raw-metadata-senteneces.txt.conll
_This file contains
**all the words of all the GCs**
tagged with its
**"lemma" & "POS"**
_
**data-sets**
-
report-manually-tagged-gcs
_Contains the extracted GCs of all the samples for each serie._
-
tagged-xml-data
_Contains the
**original xml-tagged files**
where the GCs will be extracted._
\ No newline at end of file
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