Reviewer response for version 1
The manuscript titled “MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format” addresses an important issue of extracting information from published manuscripts. 
However, the following issues must be clarified before indexing.
In the text mining section authors say that there is no tool to perform physical and logical structural analysis of PDF files. 
However, in the next paragraph they describe “Dolores” for logical structure analysis. 
Authors should describe how their method is different than Dolores.
Legends of all the figures should be more descriptive so that figures are understandable on their own. 
Each component of the figure should be described in the legend.
The results section is missing. 
Is it integrated in the discussion section? 
It is unclear what exactly the results were.
The article will be much clear if all the libraries (described on page 4 second paragraph) are described in the form of a table.
Authors should include a clear metric to estimate performance of the algorithm. 
This can be achieved by comparison with existing tools or through comparative analysis. 
A clear example showing the information extracted from several PDF files to address a biologically relevant example will be useful.
It is not clear whether the text extracted from the PDF files is actually coming from figure legends or related to the main body of the manuscript. 
Also, how is this text organized?
The authors mention that unexpected and irrelevant images were extracted. 
It is not clear how authors address that. 
It is absolutely essential to address that.
Minor corrections:
Page 2 second column: The definition of MSL is not the same as described in the abstract
Structure
Recap
Other
Recap
Recap
Todo
Todo
Todo
Weakness
Todo
Weakness
Todo
Todo
Other
Todo
Weakness
Weakness
Recap
Weakness
Todo
Structure
Weakness