- contents -- entities -- signals -- coreference -- relationships -- general guidelines -- recipe -- histopath -- radiology -
Updates and news for annotators
Please check this section regularly, to make sure that you keep up-to-date with the latest changes and instructions.
16 May 2007: A few notes for clarification; a few updates to the guidelines
Negation
Please note that we do not want negation annotated on results, interventions, investigations or any thing else, other than Condition. See negating things other than conditions. We accept that these things might sometimes be negated, but we do not want this annotating. Also, please don't change something that is obviously an intervention, result etc into a condittion so that you can negate it.
What is a result?
Results are numbers, normality, quantitative judegements and qualities that are measured by an investigation. Things like "mild", "very high", etc are results. Other things that are the findings of investigations are probably going to be Conditions. For example, "On examination abdomen distended", the word "distended" is not a result, and should be marked as a Condition. See the guideline for Result.
New guideline: staging codes
Sometimes, cancer staging codes, such as TNM codes, are given. If you think these are the result of some investigation (such as "staging"), then please mark the code as a Result. See the example in the guidelines for Result.
New guideline: chemotherapy protocols
When the word "chemotherapy" itself is used to refer to treatment, it should be annotated as a Drug. This is broadly in line with the guideline on annotating classes of drugs.
However, please do not annotate specific chemotherapy protocols as Drugs. If individual drugs are mentioned, it is ok to annotate them - but not the protocol itself. We do not want to collect protocols from the text (in part because they are available elesewhee, and in part because of their complexity).
Please see the chemotherapy guideline, which talks specifically about chemotherapy, and gives examples.
What do the asterisks mean in histopathology reports?
We are not sure! They are probably some sort of paragrpah or line separator, introduced as an artefact by the computer systems at the originating hospital. Just ignore them.
Body parts and coreference in histopathology reports
For example: should the two mentions of duodenum in different parts of a histopathology report be co-refered? Yes - they are talking about the same thing in the real world, and therefore they co-refer. Even if the document is talking about two different biopsies or sections of duodenum, the actual "duodenum" mentions are talking about the same duodenum.
10 May 2007: Interventions; Investigations; Results; typos.
There are a few points that need clarification.
Interventions
There is lots of inconsistency in what people mark as Intervention, and what they do not mark. Please, please could all annotators re-read the whole of the definition of Intervention and make sure you apply it consistently! You can find the section here
Should staging and biopsy be investigations or interventions?
If the distinction between an Intervention and an Investigation is blurre, please mark as an Investigation. See the general definition of Investigation.
What should we do about typing mistakes in a letter?
Please mark typos as misspellings, using the "Misspelt" box provided with each annotation (under the relationships boxes). Where a typist accidentally fails to put a space between two mentions (e.g. "kneepain") please annotate each separate stretch of characters appropriately ("knee" and "pain" in this example), and mark both as misspelt. See Typing mistakes.
How to annotate multi-parametered tests (such as FBC)
Some invvestigations have multiple parameters given, such as "FBC: Hb 12.1, WBC 5.4". Please mark each of the individual sub-tests or parameters as investigations, each with its own result. See: |Result.
29 March 2007: setting your annotator name in Knowtator
When you first open an annotation batch, please set your annotator name for that batch. To do this:
- Click on the "Knowtator" menu at the top
- In this, click on the "Configure" menu.
- A small configuration dialog box will open.
- Click on the "Change" button next to the "Annotator" setting.
- A "Choose default annotator" dialog box will open
- Click on "Knowtator human annotator" in the left hand pane
- A list of annotator names will appear in the right hand pane
- Click on your name in the right hand pane
- Click "OK"
- The annotator box will close
- Close the configuration dialog box by clicking the cross at its top right corner
Now, whenever you create an annotation, the "annotator" name will be filled in on the right hand side of the main window. If you do not, it will be boxed in red.
26 March 2007: histopathology and radiology
So far, most annotators will have been analysing "clinical narratives": letters, discharge summaries and so on. We will soon be asking annotators to analyse histopathology and radiology reports. This will start with a training batch, called batch-5-his-rad.
We want to use the same annotations for these, but there are a few additional points to bear in mind. Therefore, please read the following sections before annotating the histopathology and radiology reports:
9 March 2007
Revision 2.01 Please read the recent changes and points to note, as listed.
27 February 2007
Revision 2.02: Please read the recent changes and points to note, as listed.