This repository contains a collection of 622 wet lab protocols, annotated with actions, entities and relations all captured within a given sentence.
A more detailed description of the wet lab protocol corpus can be found in this paper:
An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols
Chaitanya Kulkarni, Wei Xu, Alan Ritter, Raghu Machiraju
In Proceedings of 16th Annual Conference of the North American Chapter
of the Association for Computational Linguistics: Human Language Technologies (NAACL-HLT, 2018)
Additional information regarding the action, entities and relations can be found here.
Also check out a working demo for sequence tagging and relation extraction using the methods in this repository.
All of the protocols were collected from https://www.protocols.io/ using their public APIs.
The wet lab protocol dataset annotations were created in brat and are stored in standoff format, very similar to BioNLP Shared Task standoff format: as seen here: http://2011.bionlp-st.org/home/file-formats.
Each text document in the dataset is acompanied by a corresponding annotation file. The two are associatied by using a simple file naming convention, wherein their base name (file name without the file extention) is the same: for example, the file protocol_30.ann contains annotations for the file protocol_30.txt.
Within the document, individual annotations are connected to specific spans of text through character offsets. For example, in a document beginning "Weigh 5.73 g of TCEP." the text "Weigh" is identified by the offset range 0..5. (All offsets all indexed from 0 and include the character at the start offset but exclude the character at the end offset.)
Text files are expected to have the file extension .txt and contain the text of the original protocol input into the system.
How to Make a 0.5M TCEP Stock Solution
Weigh 5.73 g of TCEP.
Add 35 ml of cold molecular biology grade water to the vial, and dissolve the TCEP.
This resulting solution is very acidic, with an approximate pH of 2.5.
The protocol texts are stored in plain text files encoded using UTF-8 (an extension of ASCII — plain ASCII texts work too). The Protocol texts contain newlines, each line indicating a single step in the protocol. The first line is always the protocol's name/title, as shown in the example above.
Annotations are stored in files with the .ann file extension. The various annotation types that may be contained in these files are discussed in the following.
All annotations follow the same basic structure: Each line contains one annotation, and each annotation is given an ID that appears first on the line, separated from the rest of the annotation by a single TAB character. The rest of the structure varies by annotation type.
Examples of annotation for an entity "Reagent" (T1), an event trigger "Action" (T2), an event (E1) and a relation (R2) are shown in the following.
T1 Reagent 111 130 fresh tissue sample
T2 Action 199 204 Weigh
E1 Action:T2 Acts-on:T4
T3 Amount 219 227 50-100mg
T4 Reagent 228 235 tissues
T5 Action 289 294 mince
E2 Action:T5 Acts-on:T6 Using:T10 Site:T8
T6 Reagent 299 305 tissue
T7 Modifier 311 328 very small pieces
R2 Mod-Link Arg1:E2 Arg2:T7
In our annotated dataset, we only ever make use of three types of annotations, each associated with their annotation ID. Those annotation IDs are described below:
T: text-bound annotation
R: relation
E: event
Detailed descriptions of each of these types of annotations are given below.
Text-bound annotations are an important category of annotation related to both entity and event annotations. Text-bound annotation identifies a specific span of text and assigns it a type.
T1 Reagent 111 130 fresh tissue sample
T2 Action 199 204 Weigh
All text-bound annotations follow the same structure. As in all annotations, the ID occurs first and is delimited from the rest of the line with a TAB character. The primary annotation is given as a SPACE-separated triple (type, start-offset, end-offset). The start-offset is the index of the first character of the annotated span in the text (".txt" file), i.e. the number of characters in the document preceding it. The end-offset is the index of the first character after the annotated span. Thus, the character in the end-offset position is not included in the annotated span. For reference, the text spanned by the annotation is included, separated by a TAB character.
Each entity annotation has a unique ID and is defined by type (e.g. Reagent or Amount) and the span of characters containing the entity mention (represented as a "start end" offset pair).
T1 Reagent 111 130 fresh tissue sample
T3 Amount 219 227 50-100mg
T4 Reagent 228 235 tissues
Each line contains one text-bound annotation identifying the entity mention in text.
Each event annotation has a unique ID and is defined by type, event trigger (the text stating the event) and arguments. We only have one type of event in our dataset, which is "Action"
T2 Action 199 204 Weigh
E1 Action:T2 Acts-on:T4
The event triggers, annotations marking the word or words stating each event, are text-bound annotations and their format is identical to that for entities. (The IDs of triggers occupy the same space as the IDs of entities, and these must not overlap.)
As for all annotations, the event ID occurs first, separated by a TAB character. The event trigger is specified as TYPE:ID and identifies the event type and its trigger through the ID. By convention, the event type is specified both in the trigger annotation and the event annotation. The event trigger is separated from the event arguments by SPACE. The event arguments are a SPACE-separated set of ROLE:ID pairs, where ROLE is one of the event- and task-specific argument roles (e.g. Acts-on, Creates, Site, etc) and the ID identifies the entity or event filling that role. Note that several events can share the same trigger and that while the event trigger should be specified first, the event arguments can appear in any order.
Binary relations have a unique ID and are defined by their type (e.g. Measure, Mod-Link) and their arguments. Relation arguments are always identified simply as Arg1 and Arg2.
R2 Mod-Link Arg1:E2 Arg2:T7
The format is similar to that applied for events, with the exception that the annotation does not identify a specific piece of text expressing the relation ("trigger"): the ID is separated by a TAB character, and the relation type and arguments by SPACE.
Instructions to view on BRAT: In order to view the protocol annotations,
- Setting up a brat server is necessary. Detailed instructions on how to setup a brat-sever can be found here: (http://brat.nlplab.org/installation.html)
- Once your installation is ready, Place the WLP-Dataset directory under "data" directory of your brat installation.
- make sure it has the right permissions using chmod as so: chmod -R g+rwx data.
- You can now access this dataset on your brat installation, through one of the supported web browsers: (http://brat.nlplab.org/supported-browsers.html).