nbclab / abbr Goto Github PK

• Abbreviation followed by comma
  • General form: full term (FT, other things)
  • Example: mean arterial pressure (MAP, in mmHg)
  • Frequency:
• Abbreviation defined after comma
  • General form: full term, FT
  • Example: (the left inferior frontal gyrus, IFG)
  • Frequency:
• Abbreviation defined after hyphen
  • General form: full term- FT
  • Example: (extending into the anterior cingulate sulcus – ACS)
  • Frequency:
• Abbreviation defined before colon
  • General form: FT: full term
  • Example: Abbreviations- BA: Brodmann's area
  • Frequency:
• Abbreviation followed by space
  • General form: full term (FT other things)
  • Example: FMRIB's Software Library (FSL version 4.1; www.fmrib.ox.ac.uk/fsl)
  • Frequency:
• Abbreviation in square brackets
  • General form: full term [FT]
  • Example: (interstimulus interval [ISI] 2.5 s)
  • Frequency:
• Brodmann areas/Abbreviations derived from some other term
  • Example: Superior frontal gyrus (BA9)
  • Example: Primary somatosensory cortex (S1)
  • Frequency:
• Full term starts with square bracket
  • General form: [full term (FT) other things]
  • Example: [Brodmann Areas (BA) 39/40 and lateral BA7, respectively]
  • Frequency:
• Full term surrounded by quotes
  • General form: "full term" (FT)
  • Example: "shared syntactic integration resource hypothesis" (SSIRH)
  • Frequency:
• Hyphen in abbreviation
  • General form: full-term (F-T)
  • Example: Resting-state functional MRI (rs-fMRI)
  • Frequency:
• Abbreviation and full term switched
  • General form: FT (full term)
  • Example: BOLD (blood oxygen level dependent)
  • Frequency:
• Multiword abbreviation (only observed in combination with letters not in full term)
  • TODO: Check that this occurs without other factors.
  • General form: full term (F T)
  • Example: anterior and posterior commissure (AC-PC line)
  • Frequency:
• Numbers in abbreviation (only observed in combination with numbers not in full term)
  • TODO: Check that this occurs without other factors.
  • General form: full term (FT1)
  • Example: statistical parametric mapping (SPM99)
  • Frequency:
• Numbers in full term
  • General form: 9-full term (FT)
  • Example: 18f-fluorodeoxyglucose (FDG)
  • Frequency:
• Underscores in abbreviation and full term
  • General form: full_term (F_T)
  • Example: IPC_inferior (IPC_i)
  • Frequency:

Numpy style, probably.

This will make feature extraction easier for bag-of-words approaches.

Permission denied (publickey).
fatal: Could not read from remote repository

In returned text after expandall and compressall the original abbreviations are currently kept. For example, after compressall the example string:

'This is a Test String (TS). I hope it is Informative (inf). '

becomes

'This is a TS (TS). I hope it is inf (inf). '

Instead, it might be better to return

'This is a TS. I hope it is inf. '

such that abbreviations are not overrepresented in the text.

I don't know if the regular expressions are getting too long, but I'm trying to run expandall on a large number of text files and it's getting stuck on some of them. @emdupre, before I dig into this, have you encountered it?

I'm guessing that this also applies to findall, but I haven't tested it.

We need test data and tests.

Mark up some documents and evaluate the tool's performance.

Now that some of the tests are up and running, I would really like to figure out how to use continuous integration so we can check PRs automatically.

Make abbr citable.