Annotation (manual and automated)

Document Reader

On the documents panel double click on an article to open the document reader. The reader allows you to read the document with some supporting tools found on the right.

 

Manually annotating the text: When you read the full text article, you can select certain important words, expressions you want to tag (annotate). When you select a word the annotation categories are visualized above the selected text, you have to select the category so the selected text will be added to the given category.

Preannotation: The 'preannotation' icon will allow you to tag all the text elements, which have been already added to the system. The HubScience team continually updates the learner for the annotation of biomedical texts. HubScience can also manage dictionaries (wordpacks) containing list of text elements, these can also be added to the system.

 

Hubscience wordpack - this is a delicately compiled list of words with categories, synonyms, abbreviation and lot of other properties. Typically a wordpack is domain specific.

 

User-defined wordpack - whenever you annotate something it gets into your project wordpack automatically and preannotation include it. The project depending wordpacks might contain the most specific and valuable information about the topic.

 

Manual Annotation

When you read the full text article, you can select certain important words, expressions you want to tag (annotate). When you select a word the annotation categories are visualized above the selected text, you have to select the category so the selected text will be added to the given category.

Preannotation Rules

Besides the auto annotation rules, and the manual connecting, Hubscience gives you the opportunity to define your own annotation rules. All rules effective after preannotation.

Add, Edit or Delete a rule

Click New button to add a new rule, or click the Edit button to edit an existing one.

Label (required): name of the rule

Direction (required): direction of the connection - before or after

Text between connected annotations must be: text, which connects the annotations

Source category (main, sub) (required): category of the first annotation you would like to connect (according to the direction)

Destination category (main, sub) (required): category of the second annotation you would like to connect (according to the direction)

You will see the new connections after the next preannotation.

Click on the Delete button to delete an existing rule. After the next preannotation, the connections resulted by the deleted rule will be deleted.

Automated Annotation

The 'preannotation' icon will allow you to tag all the text elements, which have been already added to the system. The HubScience team continually updates the learner for the annotation of biomedical texts. HubScience can also manage dictionaries (wordpacks) containing list of text elements, these can also be added to the system.

Info Panel

The side panel is designed to give you plenty of information during reading.

 

The info panels shows relevant general statistical and meta-information of the document.

 

In addition, during annotation the selected word or text element is looked up in Wikipedia or Wikidata providing more information about the specific terms helping students or  users inexperienced at a given topic.

On the info panel the images are listed for an easier review.

  • Annotation: Select an annotation and see its category and subcategory. You can delete here this annotation or search in situ with the "Annotation All" button.

  • Subject: Select an annotation and see its subject and the properties.

  • Run Advanced Query: Select an annotation and run a query from here with its subject. You will see the results on the "Advanced Query Result" page.

  • Note: You can add notes to each annotated word. (free text)

Connections (auto and manual)

Auto

Hubscience is capable of connecting annotations according to the following rules (with examples):

  • infusion of (method / administration) taurocholate (Chemical / Name)

  • ... kit (Labware / Name) Company name (Additional / Company)

  • (chemical / name) were isolated from (biology / *)

  • (Biology / *) contains (Chemical / Name)

  • sodium pyrophosphate (Chemical / Name) 50µm (Result / Data)

Manual - Simple

It is possible to manually connect to annotations. It is useful when you would like to connect e.g. a name with a description. Click on the annotation you would like to connect, and press ALT on the keyboard. A link icon will appear next to the selected annotation. This will be the parent. Click on the other annotation, that will be the Child.

 
Manual - Abbreviation

It is useful when you would like to connect an abbreviation with its long name in the document reader. Click on an annotation and press control, then click on the abbreviation. You get a message of the successful addition, but you won't see the result until the next preannotation. 

Note that this is not a normal connection, it is not shown among the connections, but on the wordcard in the dictionary!

Edit or Delete Connection

In graph mode click on the arrow to edit label or delete the connection.

Operations

Without selecting an annotation, the sidebar shows the number of annotations in the actual document and the filter possibilities.

  1. Delete all: delete all annotations.

  2. Export CSV: export all subjects to a CSV file.

  3. Search in dictionary: perform a search within the document

  4. Time Range: Time Range: it is possible to show annotations only in a specified time range.
    Select the start and the end date with the help of a popup calendar.

  5. Type: 

    • All - auto and manual

    • Auto - auto only (preannotated)

    • Manual - manual only​

  6. Category:​

    • Simple - choose a category/subcategory from the pie chart​

    • Advanced - select or deselect categories/subcategories​

  7. Member:

    • All​

    • Select one whose annotations should be visible by clicking the other member(s) name

Preannotate All Documents

The “Preannotate All Documents” button on the sidebar of the Documents screen will allow you to preannotate all your documents at the same time.

Remove Annotations

  • To remove an annotation select it in the document reader, and then click on "Delete Annotation".

  • To remove all annotations from a document simply click "Delete All" on the sidebar.