Update README and resource text

README.md

@@ -4,12 +4,10 @@
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3660006.svg)](https://doi.org/10.5281/zenodo.3660006) [![Build Status](https://travis-ci.com/titipata/pubmed_parser.svg?branch=master)](https://travis-ci.com/titipata/pubmed_parser)
 
 Pubmed Parser is a Python library for parsing the [PubMed Open-Access (OA) subset](http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/)
- , [MEDLINE XML](https://www.nlm.nih.gov/bsd/licensee/) repositories, and [Entrez Programming Utilities (E-utils)](https://eutils.ncbi.nlm.nih.gov/). It uses `lxml` library to parse this information into a Python dictionary which can be easily used for research such in text mining and natural language processing pipelines. See
- [wiki page](https://github.com/titipata/pubmed_parser/wiki) on how to download and
- process dataset using the repository.
+ , [MEDLINE XML](https://www.nlm.nih.gov/bsd/licensee/) repositories, and [Entrez Programming Utilities (E-utils)](https://eutils.ncbi.nlm.nih.gov/). It uses `lxml` library to parse this information into a Python dictionary which can be easily used for research such in text mining and natural language processing pipelines.
 
-For available APIs and details about the dataset, please see [documentation page](http://titipata.github.io/pubmed_parser/) for more details.
-Below, we list some of the core funtionalities and examples code.
+For available APIs and details about the dataset, please see our [wiki page](https://github.com/titipata/pubmed_parser/wiki) or
+ [documentation page](http://titipata.github.io/pubmed_parser/) for more details. Below, we list some of the core funtionalities and examples code.
 
 ## Available Parsers
 

docs/resources.rst

@@ -2,15 +2,14 @@
 Resources
 =========
 
-Here are some useful resources for downloading data.
+Here are some useful resources for downloading MEDLINE and PubMed Open Access (PubMed OA) XML data.
 
+Links to download PubMed OA and MEDLINE dataset
+-----------------------------------------------
 
-Links to download Pubmed and MEDLINE dataset
---------------------------------------------
+Below, we provide links for downloading PubMed OA and MEDLINE data
 
-Here are links for downloading PubMed OA and MEDLINE data
-
-- `PubMed Open-Access (OA) <http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/>`_ dataset is available at ``http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/``. Here is the `FTP link <ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/>`_ for downloading the bulk of dataset. You can check `oa_bulk folder <ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk//>`_ to see the full tar files.
+- `PubMed Open-Access (OA) <http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/>`_ dataset is available at ``http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/``. Here is the `FTP link <ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/>`_ for downloading the bulk of dataset. In the FTP link, you can go to `oa_bulk folder <ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/>`_ to see the full available tar files.
 - the MEDLINE XMLs are available here ``ftp://ftp.nlm.nih.gov/nlmdata/.medleasebaseline/gz/``
 - the MEDLINE XMLs weekly updates are available here ``ftp://ftp.nlm.nih.gov/nlmdata/.medlease/gz/``
 - MEDLINE Document Type Definitions (DTDs) file is available at this `link <https://www.nlm.nih.gov/databases/dtd/>`_. We can use it to see available tags from a given MEDLINE XML.
@@ -19,17 +18,17 @@ Here are links for downloading PubMed OA and MEDLINE data
 Download PubMed OA figures
 --------------------------
 
-Here, we explain how to download PubMed OA figures corresponded to the parsed information
+Here, we explain how to download PubMed OA figures corresponded to the parsed information from ``parse_pubmed_caption`` function
 
 - In ``pubmed_parser``, you can use ``parse_pubmed_caption`` to parse figures (to be specific ``figure_id``) and captions corresponding to a manuscript. 
-- To download the images corresponding to a given ``PMC`` or ``PMID``, you can download a CSV file from ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.csv`` first. - The file will have columns ``PMID``, ``Accession ID`` (``PMC``), and ``File`` where it looks something like ``oa_package/08/e0/PMC13900.tar.gz``.
-- You can then download a tar file for a given ``PMID`` or ``PMC`` from ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/08/e0/PMC13900.tar.gz``. You can check out ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/`` to get all the access for tar files.
+- To download the images corresponding to a given ``PMC`` or ``PMID``, you can download a CSV file from ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.csv`` first. The file will have columns ``PMID``, ``Accession ID`` (``PMC``), and ``File``. In ``File`` column, you can see the path to download a tar file of an XML and corresponding figures in the following format ``oa_package/08/e0/PMC13900.tar.gz``.
+- You can use the path to download a tar file for a given ``PMID`` or ``PMC`` in a following format: ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/08/e0/PMC13900.tar.gz``. If you want to download all the tar files, check out ``ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/`` to see all the files.
 
 
 PMC Copyright Notice
 --------------------
 
-Wehn you use Pubmed Parser to parse information from the website, do not download them as a bulk. Your IP might get banned from doing it.
+When you use Pubmed Parser to parse information from the website, do not download them as a bulk. Your IP might get banned from doing it.
 Please see copyright notice when you scrape data from website `here <https://www.ncbi.nlm.nih.gov/pmc/about/copyright/#copy-PMC/>`_.
 
 Alternative implementation of MEDLINE parsers