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Add small improvements to README.md (#1)
* Add small improvements to README.md Markdown only makes new paragraphs on a double new-line. Keep each sentence in a line for ease of editing and diffing. Remove all trailing white space. Clarify Sciencer core concepts and its general usage. * Improve README Add filter description to example Add white space on tables Co-authored-by: Diogo Rato <[email protected]>
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README.md

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Sciencer Toolkit
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</h1>
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<h4 align="center">A smarter way to find new articles.</h4>
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<h4 align="center">A smarter way to find articles.</h4>
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<p align="center">
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<a href="https://pypi.org/project/sciencer-toolkit/">
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<img src="https://img.shields.io/pypi/dm/sciencer-toolkit.svg?style=flat-square&logo=github&logoColor=white"
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<a href="https://pypi.org/project/sciencer/">
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<img src="https://img.shields.io/pypi/dm/sciencer.svg?style=flat-square"
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alt="GitHub pull requests"></a>
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<a href="https://github.com/SciencerIO/sciencer-toolkit/issues">
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<img src="https://img.shields.io/github/issues-raw/SciencerIO/sciencer-toolkit.svg?style=flat-square&logo=github&logoColor=white"
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<img src="https://img.shields.io/github/issues-pr-raw/SciencerIO/sciencer-toolkit.svg?style=flat-square&logo=github&logoColor=white"
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alt="GitHub pull requests"></a>
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<a href="https://github.com/SciencerIO/sciencer-toolkit/LICENSE">
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<img src="https://img.shields.io/github/license/SciencerIO/sciencer-toolkit.svg?style=flat-square&logo=github&logoColor=white"
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<img src="https://img.shields.io/github/license/SciencerIO/sciencer-toolkit.svg?style=flat-square"
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alt="License: MIT License"></a>
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</p>
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<p align="center">
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<a href="#about">About</a> •
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<a href="#usage">Usage</a> •
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<a href="#roadmap">Roadmap</a> •
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<a href="#contributing">Contributing</a> •
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<a href="#license">License</a>
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<a href="#about">About</a> -
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<a href="#usage">Usage</a> -
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<a href="#roadmap">Roadmap</a> -
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<a href="#contributing">Contributing</a>
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</p>
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<p align="center">
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<a href="#collectors">Collectors</a>
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<a href="#expanders">Expanders</a>
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<a href="#filters">Filters</a>
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<a href="#collectors">Collectors</a> -
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<a href="#expanders">Expanders</a> -
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<a href="#filters">Filters</a> -
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<a href="#providers">Providers</a>
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</p>
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---
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## About
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Sciencer Toolkit enables researchers with the tools to **programmatically conduct a literature review** using an intuitive yet flexible interface.
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Sciencer Toolkit enables researchers to **programmatically conduct a literature review** using an intuitive yet flexible interface.
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Sciencer iteratively identifies a set of papers using **Expanders**. Each expander enlarges a set of papers to a larger set (e.g. using authors, citations, references, etc...). At the end of each iteration, each new paper needs to satisfy a series of **Filters** to be accepted. The initial set of papers is created using **Collectors** (e.g. by paper doi, author name).
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At its core, Sciencer collects sets of papers.
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The initial set of papers is created through the use of **Collectors** (e.g. paper doi, author name).
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Then, Sciencer iteratively finds new papers using **Expanders** (e.g. authors, citations, references).
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Finally, new found papers need to satisfy a series of **Filters** in order to be accepted into the current set.
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Being iterative in nature, Sciencer allows you to repeat the above steps has many times as you'd like.
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This project was motivated by the absence of tools to automate systematic reviews using clear and well-defined criteria. Still, for literature reviews that do not need to follow specific criteria, there are a several tools that can help to discover new papers.
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This project was motivated by the absence of tools to automate systematic reviews using clear and well-defined criteria.
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Still, for literature reviews that do not need to follow specific criteria, there are a several tools that can help to discover new papers.
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## Usage
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sciencer.add_provider(SemanticScholarProvider())
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# Define collectors
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sciencer.add_collector(sciencer.collectors.CollectByAuthorID(...))
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sciencer.add_collector(sciencer.collectors.CollectByDOI(...))
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## this collector will gather all known papers authored by "John Doe" into de set
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sciencer.add_collector(sciencer.collectors.CollectByAuthorID("John Doe"))
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## this collector will collect the paper with DOI "1234567890" into the set
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sciencer.add_collector(sciencer.collectors.CollectByDOI("1234567890"))
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# Define expanders
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## this expander will gather all known papers written by authors in the current set.
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sciencer.add_expander(sciencer.expanders.ExpandByAuthors())
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# Define filters
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## this filter will reject papers that were published before 2010 and after 2030
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sciencer.add_filter(sciencer.filters.FilterByYear(min_year=2010, max_year=2030))
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## this filter will reject all the appers that do not have the word social on the abstract
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sciencer.add_filter(sciencer.filters.FilterByAbstract("social"))
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# Run one iterations
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# Run one iteration
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results = sciencer.iterate()
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```
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## Collectors
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| Name | Description | Parameters |
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| ----------- | :---------- | :--------- |
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| Author ID | Collects all the papers written by an author | Authors's SemanticScholar ID |
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| Paper DOI | Collects a paper by its DOI | Paper's DOI |
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| Name | Description | Parameters |
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| --------- | :------------------------------------------- | :--------------------------- |
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| Author ID | Collects all the papers written by an author | Authors's SemanticScholar ID |
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| Paper DOI | Collects a paper by its DOI | Paper's DOI |
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<p align="right">(<a href="#top">back to top</a>)</p>
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## Expanders
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| Name | Description |
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| ----------- | :---------- |
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| Authors | Expands a paper by its authors |
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| Name | Description |
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| ------- | :----------------------------- |
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| Authors | Expands a paper by its authors |
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<p align="right">(<a href="#top">back to top</a>)</p>
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## Filters
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| Name | Description | Parameters |
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| ----------- | :---------: | ------------ |
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| By Year | Filters a paper by its year | The lowest acceptable year (inclusive) <br> The highest acceptable year (inclusive) |
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| By Abstract Words | Filters a paper by its abstract | The collection of words the abstract should include (at least one) |
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| Name | Description | Parameters |
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| ----------------- | :------------------------------ | ----------------------------------------------------------------------------------- |
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| By Year | Filters a paper by its year | The lowest acceptable year (inclusive) <br> The highest acceptable year (inclusive) |
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| By Abstract Words | Filters a paper by its abstract | The collection of words the abstract should include (at least one) |
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<p align="right">(<a href="#top">back to top</a>)</p>
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## Providers
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| Name | Provider | Features |
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| :----------: | :----------: | :----------- |
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| Semantic Scholar | [Semantic Scholar Academic Graph API](https://www.semanticscholar.org/product/api) | **Search by Author** (Name, S2ID) <br> **Search By Paper ID** (S2ID, DOI, ArXiv, MAG, ACL, PubMed, Corpus)
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| DBLP | [DBLP Search API](https://dblp.org/faq/How+to+use+the+dblp+search+API.html) | *Work in Progress*
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| Name | Provider | Features |
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| :--------------: | :--------------------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------------------- |
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| Semantic Scholar | [Semantic Scholar Academic Graph API](https://www.semanticscholar.org/product/api) | **Search by Author** (Name, S2ID) <br> **Search By Paper ID** (S2ID, DOI, ArXiv, MAG, ACL, PubMed, Corpus) |
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| DBLP | [DBLP Search API](https://dblp.org/faq/How+to+use+the+dblp+search+API.html) | *Work in Progress* |
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<p align="right">(<a href="#top">back to top</a>)</p>
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## Roadmap
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- [ ] Create Paper's and Author's Cache
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- [x] Add Bulk Expanders (to avoid redundancy)
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- [ ] Add support for multithreading
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- [ ] Add support for multithreading
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- [ ] Add Collectors
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- [ ] Add Collect by Venue/Proceedings
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- [ ] Add Expanders
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## Contributing
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Want to **add a new provider, filter or expander**? Looking to improve **the core functionality of sciencer toolkit**. We would look forward to include your contributions in the toolkit! If you have a suggestion that would improve the toolkit, please fork the repo and create a new pull request:
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1. Fork the Project
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2. Create your Feature Branch
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3. Commit your Changes
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4. Push to the Branch
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5. Open a Pull Request
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Want to **add a new provider, filter or expander**?
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Looking to improve **the core functionality of sciencer toolkit**.
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We look forward to include your contributions in the toolkit!
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If you have a suggestion that would improve the toolkit just send us a Pull Request!
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If you are looking for an additional collector/filter/expander/provider or just want to report a bug, you can also simply open an issue with the tag "enchament" or "bug", respectively.
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