• Introduction
• Project Value
• Client Expectation
• System Diagram
• User Interface Prototype
• User Story Map
• Milestones
• Schedule
• Progress
• Risk Management
• Team Member Roles
• Communiaction Tools
• Development Environment
• Development Tools
• Decision Make Procedures
• Testing
• Meeting Agendas
• Audit Presentation
• Other Resources
• Handover

Our project aims to automate taxonomic data capture from scientific reports, something which is currently performed manually. This information can then be uploaded to searchable databases where it can be accessed by the public. Automating this process will save our client time, effort and money which can be better spent elsewhere. Our project will develop a web-based application, which can extract taxonomic information from XML or PDF articles, output a straightforward format which the client is then able to check, edit. XML articles could be download from publishing houses under Pensoft(https://zookeys.pensoft.net/articles) and PDF articles could should be academic articles in biological area. Our online application is deployed on https://taxonomic-tl.herokuapp.com . Users could upload the above artilces and download the results.

Having a comprehensive database of taxa data is useful to those studying biology as they can easily search the database to find relevant materials describing the taxa they are studying. These biological studies can help with sustainable management of biodiversity, conservation/protection of species, biosecurity, management of invasive species and much more. Our project will build an web-based automatic data collection application. Therefore, it can improve the data collection efficiency for Australian Biological Resources Study(ABRS), optimise extraction accuracy, reduce their labor consumption and save a lot of money.

The client expects us to achieve functionality in terms of analysing documents in pdf or xml form and returning taxonomic information in a straightforward format, which the client is then able to check, edit. The program should be intuitive, accurate and time-saving.

General:

• CSV output
• Passed user acceptance testing
• Well formatted output
• Generate a report for lessons learnt and issues in the process of extracting data.

UI:

• Specify UI input and output preview display
• Design all the windows needed. Editable output

PDF:

• Acceptable level of name border recognition
• Reference parsing
• Field association (connecting relevant information)

XML:

• Changing output format to csv.
• Adding and changing output fields according to clients’ requirement.
• Mapping with the standard schema.
• Testing more cases from Zookeys, and other publishers’ articles who also use TaxPub xml structure. Make improvements on the extraction accuracy.
• Analysing and report on the failure situation.

Server:

• Getting contact with ANU to know if we could establish a server in ANU.
• Studying informations about other platforms where we could implement server, such as Heroku.
• Learning server knowledges and give a break-down plan of implementation.

Testing:

• Main function testing
• Client acceptance testing
• User's manual

Weeks 2-3:

• Re-establish communication with client
• Create plan for the semester
• Update necessary documentation (updating landing page, set new google files, risk register, milestones, schedules. )
• Prepare for audit (ppt)
• Getting contact with ANU to know if we could establish a server in ANU. If not applicable, research other server platform (Heroku)
• Studying on the knowledge of server deployment.
• Specify UI input and output preview display.
• Change output format to csv

Weeks 4-5:

• Improve UI (output display)
• Work on parsing bibliography references (PDF)
• Adding and changing output fields according to clients’ requirement and feedback. Working on different cases of ZooKeys (XML)
• Try to reduce reliance on webservers
• Studying on the knowledge of server deployment. Making a breakdown plan of server deployment. Kick-off.

Weeks 5-6:

• Improve UI (output display)
• Improve UI (input display)
• Attempt to increase "border word" list / Integrate other name detection (PDF)
• Add some holotype/coordinate detection (PDF)
• Working on different cases of Zookeys. Making imporvements on accuracy. Make the output in the standard schema (XML)
• Continue deploying server, link UI with server (Server)
• Design testing for accuracy. Start build testing accuracy (Testing)
• Prepare for audit

Mid-break:

• Improve UI (editable output)
• Improve UI (output display)
• Improve UI (input display)
• Try to link different attributes within text (eg genders with holotypes, holotypes with species) (PDF)
• Try to highlighting the extracted information in the original pdf (PDF)
• Working on the cases of species combination, or changing species' category (XML)
• Finishing mapping original output to standard schemas(XML)
• Working on different publishers' cases of TaxPub. Making imporvements on accuracy. Make the output in the standard schema (XML)
• Continue deploying server, link backend with server. Provide the website to clients which they could use (Server)
• Testing accuracy.

Week 7-8:

• Improve UI (editable output)
• PDF output in standard schema (PDF)
• Server updates to make sure the result is stardard schema (Server)
• Finishing testing accuracy (Testing)
• Accuracy algorithm design and implement (Testing)

Week 9-10:

• Testing with client
• Acting on client feedback
• Prepare for audit
• Generate a report for lessons learnt and issues in the process of extracting data.

Week 11-12:

• Finalising project
• User acceptance testing

Semester 1

Audit 1:

• Researched relevant biology/taxonomy information
• Indentified risks.
• Created a github project.
• Communicated with clients, find the problem, underlying needs.

Audit 2:

• Created the general structure of the project and the structure of each part (frontend, backend, UI, testing).
• Made statement of work (SOW).
• Allocated tasks and roles according to the SOW.
• Created UI prototype.
• Started research GoldenGate.
• Implemented basic functions to identify new species name and genus name in the abstract of XML formatted article.

Audit 3:

• Communicated with clients about the output schema, updating clients’ needs.
• Designed poster.
• Finished the research about GoldenGate, started using NLP to process PDF articles.
• Found other taxonomic information related with new species/genus, agents and reference in XML articles, matching.
• Formatted the extracted the extracted data as clients’ needs.
• Used flask (a micro web framework written in Python) to connect with backend.
• Wrote unit test.

Semester 2

In this semester, we make a schedule for the whole semester in week2. Each week, in the group meeting, each member will put forward their own tasks according to the schedule. And report how they did according to their tasks of last week, especially analyse the reasons for the delay parts and raise new solutions. We use "issues" on github to document everyone's achievements and reflections.

Audit 1:

• Create plan for the semester
• Update necessary documentation eg.SOW, risk register, github.

Audit 2:

• Deploy the server.
• Reach agreement on plan of testing accuracy plan, and begin to build test.
• PDF could parse reference.
• XML extraction program integrated and pack outputs file into zip file
• Get populated standard schemas. Mapping XML outputs to standard schemas (in progress)
• Accpetance criteria

As the project is being implemented as part of a secure system, it is important that it does not present any new vulnerabilities to that system. This can be achieved by being considerate of the environment in which our project will be deployed and using appropriate programming techniques.

1. Email
2. Facebook Messenger

• Language:
• Backend is written in python
• Frontend uses HTML, CSS and JavaScript
• Testing:
  • Unit test during development by black/white box
  • A/B test for the final stage

1. PyCharm(Python IDE)
2. Flask(A micro web framework)
3. DreamWeaver(HTML, CSS, JavaScript)

1. Testing Design

2. Testing Plan

3. Testing Methods

4. Testing Process

5. Testing Results