PyUniProt Documentation

for version: 0.0.10

PyUniProt is python software interface developed by the Department of Bioinformatics at the Fraunhofer Institute for Algorithms and Scientific Computing SCAI to the data provided by the European Bioinformatics Institute (EMBL-EBI) on their UniProt website.

The content of UniProt and the use of PyUniProt in combination with PyBEL supports successfully scientists in the IMI funded projects AETIONOMY and PHAGO in the identification of potential drugs in complex disease networks with several thousands of relationships compiled from BEL statements.

Aim of this software project is to provide an programmatic access to locally stored UniProt data and allow a filtered export in several formats used in the scientific community. Many query functions allow search in the data and use it as pandas.DataFrame in Jupyter notebooks. We will focus our software development on the analysis and extension of biological disease knowledge networks. PyUniProt is an ongoing project and needs improvement. We are happy if you want support our project or start a scientific cooperation with us.

Fig. 1: ER model of PyUniProt database

• supported by IMI, AETIONOMY, PHAGO.

• 1. Installation
  • 1.1. System requirements
  • 1.2. Supported databases
  • 1.3. Install software
  • 1.4. Changing database configuration
• 2. Quick start
• 3. Tutorial
• 4. Query functions
  • 4.1. Before you query
  • 4.2. entry
  • 4.3. disease
  • 4.4. disease_comment
  • 4.5. other_gene_name
  • 4.6. alternative_full_name
  • 4.7. alternative_short_name
  • 4.8. accession
  • 4.9. pmid
  • 4.10. organismHost
  • 4.11. dbReference
  • 4.12. feature
  • 4.13. function
  • 4.14. keyword
  • 4.15. ec_number
  • 4.16. subcellular_location
  • 4.17. tissue_specificity
  • 4.18. tissue_in_reference
• 5. Query properties
  • 5.1. dbreference_types
  • 5.2. taxids
  • 5.3. datasets
  • 5.4. feature_types
  • 5.5. subcellular_locations
  • 5.6. tissues_in_references
  • 5.7. keywords
• 6. RESTful API
• 7. UniProt
  • 7.1. About
  • 7.2. Citation
  • 7.3. Links
• 8. Benchmarks
  • 8.1. MySQL/MariaDB

Reference

• Query
  • Examples
  • Methods by examples
  • Properties
  • Query Manager Reference
• Data Models
  • Entry
  • Accession
  • OtherGeneName
  • Sequence
  • Disease
  • DiseaseComment
  • AlternativeFullName
  • AlternativeShortName
  • Accession
  • Pmid
  • OrganismHost
  • DbReference
  • Feature
  • Function
  • Keyword
  • ECNumber
  • SubcellularLocation
  • TissueSpecificity
  • TissueInReference

Project

• 1. Roadmap
• 2. Technology
  • 2.1. Versioning
  • 2.2. Testing in PyUniProt
    • 2.2.1. Tox
    • 2.2.2. Continuous Integration
    • 2.2.3. Code Coverage
  • 2.3. Distribution
    • 2.3.1. Versioning
    • 2.3.2. Deployment

Acknowledgment and contribution to scientific projects

Software development by:

• Christian Ebeling

The software development of PyUniProt by Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) is supported and funded by the IMI (INNOVATIVE MEDICINES INITIATIVE) projects AETIONOMY and PHAGO. The aim of both projects is the identification of mechnisms in Alzhiemer’s and Parkinson’s disease in complex biological BEL networks for drug development.

Indices and Tables

• Index
• Module Index
• Search Page