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See the Notebook at: https://github.com/JavierLopatin/PhenoPY/blob/master/phenopy/ExampleData.ipynb About Phenological analysis of Remote Sensing data with Python
- phenopy
- Command Line Usage
- Library Usage
- Initial setup
- Config
- Contributing
- References
- Citing Phenopy
phenopy was developed using Python 3.9 and functions to perform phenotype similarity scoring by semantic similarity. phenopy is a lightweight but highly optimized command line tool and library to efficiently perform semantic similarity scoring on generic entities with phenotype annotations from the Human Phenotype Ontology (HPO).
score
phenopy is primarily used as a command line tool. An entity, as described here, is presented as a sample, gene, or disease, but could be any concept that warrants annotation of phenotype terms. Use phenopy score to perform semantic similarity scoring in various formats. Write the results of any command to file using --output-file=/path/to/output_file.txt 1.Score similarity of entities defined by the HPO terms from an input file against all the OMIM diseases in .phenopy/data/phenotype.hpoa. We provide a test input file in the repo. The default summarization method is to use --summarization-method=BMWA which weighs each diseases' phenotypes by the frequency of a phenotype seen in each particular disease. Output: 2.Score similarity of entities defined by the HPO terms from an input file against all the OMIM diseases in .phenopy/data/phenotype.hpoa, to use the non-weighted summarization method use --summarization-method=BMA which uses a traditional best-match average summarization of semantic similarity scores when comparing terms from record a with terms from record b. Output: 3.Score similarity of an entities defined by the HPO terms from an input file against a custom list of entities with HPO annotations, referred to as the --records-file. Both files are in the same format. Output: 4.Score pairwise similarity of entities defined by the HPO terms from an input file using --self. Output: 5.Score age-adjusted pairwise similarity of entities defined in the input file, using phenotype mean age and standard deviation defined in the --ages_distribution_file, select best-match weighted average as the scoring summarization method --summarization-method BMWA. Output: The phenotype age file contains hpo-id, mean, sd as tab separated text as follows
score
Generate the hpo network and supporting objects: Then, instantiate the Scorer class and score hpo term lists. Output:
miscellaneous
The library can be used to prune parent phenotypes from the phenotype.hpoa and store pruned annotations as a file
phenopy is designed to run with minimal setup from the user, to run phenopy with default parameters (recommended), skip ahead to the Commands overview.
This section provides details about where phenopy stores data resources and config files. The following occurs when you run phenopy for the first time.
1.phenopy creates a .phenopy/ directory in your home folder and downloads external resources from HPO into the $HOME/.phenopy/data/ directory.
2.phenopy creates a $HOME/.phenopy/phenopy.ini config file where users can set variables for phenopy to use at runtime.
While we recommend using the default settings for most users, the config file can be modified: $HOME/.phenopy/phenopy.ini.
To run phenopy with a different version of hp.obo, set the path of obo_file in $HOME/.phenopy/phenopy.ini.
We welcome contributions from the community. Please follow these steps to setup a local development environment.
To run tests locally:
The underlying algorithm which determines the semantic similarity for any two HPO terms is based on an implementation of HRSS, published here.
Please use the following Bibtex to cite this software.
16 giu 2023 · phenopy. phenopy was developed using Python 3.9 and functions to perform phenotype similarity scoring by semantic similarity. phenopy is a lightweight but highly optimized command line tool and library to efficiently perform semantic similarity scoring on generic entities with phenotype annotations from the Human Phenotype Ontology ...
Phenolopy (phenology + python) is a python-based library for analysing satellite timeseries data. Phenolopy has been designed to investigate the seasonality of satellite timeseries data and their relationship with dynamic vegetation properties such as phenology and temporal growth patterns.
Welcome to phonopy. #. Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels. Phono3py is another open source package for phonon-phonon interaction and lattice thermal conductivity calculations.
17 apr 2019 · To reduce variance and speed up to process of behavioral analysis, Balzani et al. developed Phenopy, an open-source software for recording and analyzing behavioral data for phenotyping. The software allows for recording components of a behavioral task in combination with electrophysiology data.
30 mag 2019 · pyPheonology is a software package for building plant phenology models. It has numpy at it’s core, making model building and prediction extremely fast. The core code was written to model phenology observations from the National Phenology Network, where abundant species have several thousand observations. The API is inspired by ...
