+----------------+-------------+-----------------------+-------------------------------------+-----------------------------------------+
| entity_topic   | entity_type | entity_name           | example                             | description                             |
+----------------+-------------+-----------------------+-------------------------------------+-----------------------------------------+
| README         | version     | SCRUBBER 3.1-SNAPSHOT |                                     |                                         |
| README         | version     | cTAKES 1.2.2          |                                     |                                         |
| global         |             |                       |                                     |                                         |
| global         | variable    | @DATASET              | select TEST into @DATASET           | (TRAIN | TEST) select dataset           |
| global         | variable    | @CSV_DIR              | select /tmp/mysql/ into @CSV_DIR    | call csvwrite(table)                    |
| global         | variable    | @LOG_LEVEL            | select 1 into @LOG_LEVEL            | turn on printing log to console         |
| shell          |             |                       |                                     |                                         |
| shell          | procedure   | mem                   | call mem                            | get schema +memory usage                |
| shell          | procedure   | ps                    | call ps                             | show current sql process                |
| shell          | procedure   | csvread               | call csvread(WordToken)             | csv->table                              |
| shell          | procedure   | csvwrite              | call csvwrite(WordToken)            | table->csv                              |
| logging        |             |                       |                                     |                                         |
| logging        | table       | etl_log               | call log | tail | etime             | scrubber application log                |
| logging        | procedure   | log                   | call log (tablename, message)       | add new log event                       |
| logging        | procedure   | tail                  | call tail                           | print recent log events                 |
| logging        | procedure   | etime                 | call etime                          | print elapsed time from log             |
| ctakes         |             |                       |                                     |                                         |
| ctakes         | uima        | Annotation            | desc table | csvread | csvwrite     | UIMA base class                         |
| ctakes         | ->          | Sentence              | desc table | csvread | csvwrite     | sequence of annotation tokens           |
| ctakes         | ->          | Calculation           | desc table | csvread | csvwrite     | TermFrequency                           |
| ctakes         | ->          | OntologyMatch         | desc table | csvread | csvwrite     | UMLS, Regex, and Private dictionaries   |
| ctakes         | type        | BaseToken             | desc table | csvread | csvwrite     | CTAKES base class                       |
| ctakes         | ->          | NumToken              | desc table | csvread | csvwrite     | token is a number                       |
| ctakes         | ->          | WordToken             | desc table | csvread | csvwrite     | token is a word                         |
| Classification |             |                       |                                     |                                         |
| Classification | table       | Class                 | desc table | show index             | PHI| NA                                 |
| Classification | table       | Sample                | desc table | show index             | Class ( NumToken | WordToken )          |
| Classification | table       | Feature               | desc table | show index             | Lexical | Stat | Pattern | Ontology     |
| Classification | table       | FeatureBin            | desc table | show index             | POS | UMLS | regex                      |
| Classification | table       | FeatureMatrix         | desc table | show index             | (row,col) = (Sample,Feature)            |
| Classification | table       | FeatureMatrixOnt      | desc table | show index             | (row,col) = (Sample,OntologyMatch)      |
| Features       |             |                       |                                     |                                         |
| Features       | type        | Feature               | Lexical | Stat | Pattern | Ontology |                                         |
| Features       | ->          | Lexical               | POS* | Capital | cTAKES*            |                                         |
| Features       | ->          | Lexical               | POS*                                | Part of Speech (BIN)?                   |
| Features       | ->          | Lexical               | Capital                             | Token Capitalization                    |
| Features       | ->          | Lexical               | cTAKES*                             | (context dependent)                     |
| Features       | ->          | Stat                  | TF* | TokenLength | BagOfWords      |                                         |
| Features       | ->          | Stat                  | TF*                                 | Term Frequency (POS)?                   |
| Features       | ->          | Stat                  | TokenLength                         | length(token)                           |
| Features       | ->          | Stat                  | BagOfWords                          | #OntologyMatches per ontology           |
| Features       | ->          | Pattern               |                                     |                                         |
| Features       | ->          | Pattern               | Beckwith Regular Expressions        | Beckwith et al. 2006                    |
| Features       | ->          | Pattern               | custom                              | custom regex.list                       |
| Features       | ->          | Ontology              |                                     |                                         |
| Features       | ->          | Ontology              | UMLS                                | Hl7|ICD|LOINC|MESH|RXNORM|SNOMED|COSTAR |
+----------------+-------------+-----------------------+-------------------------------------+-----------------------------------------+