Xpress_parse

Help a user or a group of users to semi-automatically parse and select (and label) papers searched on Web Of Science based on their abstracts.

Description

Keeping up to data with the scientific literature can be overwhelming and this is also tedious today to go through many articles and find those relevant to one's research, for example to write a review.

This tools simply takes as input the article records downloaded for given search(es) on the Web Of Science (woscc) website and interactively queries the user by showing the abstract and asking for input whether this article record should be skipped, or kept and if kept, whether it should be labeled.

It can help a team of humans to go through all studies retrieved using a search on the Web Of Science website, and selecting some based on their abstracts. I can be useful to find studies that could have been missed by searching on SRA and EBI if one is looking for papers with sequences.

Install

pip install Xpress-parse

or

git clone https://github.com/FranckLejzerowicz/Xpress_parse.git
cd Xpress_parse
pip install -e .

Input

One or more than one input file can be passed to -i or --i-script but each file must be in the format as downloaded from WoS basic search:

• "Export" must be in tab delimited format

• "Record Content" must be Full Record

By default the record file downloaded are named savedrecs.txt and it is advised to either rename this file, or to place each in a folder documenting the search it originates from, e.g. a folder structure:

.
└── woscc_searches
    ├── plastic_microbes
    │   ├── readme.txt     # a file explining this search
    │   └── savedrecs.txt  # the results of this search
    └── biofilm_dna
        ├── readme.txt     # a file explining this other search
        └── savedrecs.txt  # the results of this other search

Which would be:

Xpress \
   -i woscc_searches/plastic_microbes/savedrecs.txt \
   -i woscc_searches/biofilm_dna/savedrecs.txt

Outputs

An output file path can be provided (otherwise the output is placed on the working directory and named xpress_records_YYYY-MM-DD.tsv)

Xpress \
   -i woscc_searches/plastic_microbes/savedrecs.txt \
   -i woscc_searches/biofilm_dna/savedrecs.txt \
   -o my_output.tsv 

This output is a non redundant concatenation of all the input tables, with extra columns:

• file: input file or (comma-separated) input files where the record exists.
• PERSON: user who (empty if no use of option -u).
• labels: double underscore-separated ("__") labels assigned to a record.

Team work

One might ask help from colleagues to go through a large list of papers. For example, if there are 2000 papers to check and 10 people in the team, a work load of 200 papers per person is reasonable. For a given command line, the team members can use the option -u (or --p-users) multiple times, with each time for each user, but with your name first, e.g.:

Xpress \
   -i woscc_searches/plastic_microbes/savedrecs.txt \
   -i woscc_searches/biofilm_dna/savedrecs.txt \
   -o my_output.tsv \
   -u Franck \  # always put YOUR name first
   -u Kenia \
   -u Pau \
   -u Tam \
   -u Alex \
   -u Maria

This will split the records list into even-sized chunks at a rate of one chunk per user. When the chnuk selection is completed, you username will be added to the file name, e.g. xpress_records_YYYY-MM-DD_<YOURNAME>.tsv

Hence, user Kenia would need to run this command to work on another chunk of the same search(es):

Xpress \
   -i woscc_searches/plastic_microbes/savedrecs.txt \
   -i woscc_searches/biofilm_dna/savedrecs.txt \
   -o my_output.tsv \
   -u Kenia \  # that will parse over Kenia's share
   -u Franck \ # the order of the others is not important 
   -u Pau \
   -u Tam \
   -u Alex \
   -u Maria

Stop/Resume

In case you want to make a break while you go through the abstracts, just type either of exit or stop, or use the escape keyboards command CTRL-C.

You will be asked if you want to remove a study (that would have been added by mistake) and then to add a study (that you failed to add).

Then, it will write a file with a timestamp in its name, so that when the command is re-run, these studies collected before the break are re-read and the full collection updated so that you only start where you left. Note that the file written with the timestamp will be located in the same folder as the first file given to option -i (remember that you can use -i multiple times to process multiple searches).

So, if you stop and restart later, be sure to not only use the same file(s) and in the same command line, but also make sure that the first file in you command is located in the same folder as it was before you stopped! Otherwise, the parsing will restart from scratch.

Usage

Xpress -i </path/to/savedrecs.txt> [ -i </path/to/another/savedrecs_file.txt>]

Options

  -i, --i-records TEXT  Path(s) to WoS search result(s)
  -o, --o-output TEXT   Selected records (default to
                        xpress_records_YYYY-MM-DD.tsv)

  -u, --p-user TEXT     User name(s)
  -l, --p-labels TEXT   Path to file with 2 tab-separated
                        columns: keywords and labels

  --version             Show the version and exit.
  --help                Show this message and exit.

Bug Reports

contact franck.lejzerowicz@gmail.com