Re: Ideas for building a system that parses medical research publications/articles

Στις 5/6/21 1:52 μ.μ., ο/η Laura Smith έγραψε:

> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
> On Saturday, 5 June 2021 10:49, Achilleas Mantzios <achill(at)matrix(dot)gatewaynet(dot)com> wrote:
>
>> Hello
>>
>> I am imagining a system that can parse papers from various sources
>> (web/files/etc) and in various formats (text, pdf, etc) and can store
>> metadata for this paper ,some kind of global ID if applicable, authors,
>> areas of research, whether the paper is "new", "highlighted",
>> "historical", type (e.g. Case reports, Clinical trials), symptoms (e.g.
>> tics, GI pain, psychological changes, anxiety, ), and other key
>> attributes (I guess dynamic), it must be full text searchable, etc.
>>
>> I am at the very beginning in this and it is done on a fully volunteer
>> basis.
>>
>> Lots of questions : is there any scientific/scholar analysis software
>> already available? If yes and is really good and open source , then this
>> will influence the rest of decisions. Otherwise , I'll have to form a
>> team that can write one, in this case I'll have to decide DB, language,
>> etc. I work 20 years with pgsql so it is the natural choice for any kind
>> of data, I just ask this for the sake of completeness.
>>
>> All ideas welcome.
> Hello Achilleas
>
> Not wishing to be discouraging, but you have very ambitious goals for what sounds like a one-person project ?
>
> You are effectively looking at competing with platforms such as Elsevier Scopus/Scival which are market-leaders in the area for good reason (i.e. it takes a lot of manpower to write algorithms, manage metadata etc., and the only way to consistently maintain that manpower is to employ people, lots of them). There are also things like Google Scholar around the place.
>
> I think before starting on the technical side of Postgres etc., the honest truth is that you need to do more planning, both in terms of implementation and long-term sustainability.
>
> For example, before we even get to metadata, you talk of various sources and formats. Have you considered licensing issues ? Have you considered how to keep the dataset clean ? (If you are thinking you can just scrape the web, then you'll be in for a surprise).

All I got is some very vague descriptions coming from either ppl from
the advocacy side or the medical side.

I got no idea on the legal status of those documents, as you know some
are covered by the artistic license (a few in PubMed) some not,

I am not a lawyer. The data are not to be stored locally AFAIK, so only
metadata will be kept locally and can be reset, refreshed, amended, etc

Parsing will be equivalent to a one-off human reading the article on the
web. There is a lawyer handling all those. From the whole network of ppl
interested in this whole endeavor,  I am the only guy with DB/software
knowledge, hence why I volunteered.

I know its a huge work, but you are missing a point. Nobody wishes to
compete with anyone. This is a about a project, a parent-advocacy
non-profit that *ONLY* aims to save the sick children (or maybe also
very young adults) of a certain spectrum . So the goal is to make the
right tools for researchers, clinicians and parents. This market is too
small to even consider making any money out of it, but the research is
still very expensive and the progress slower than optimum.

> Laura