Okay.
So my name is
Cozette, I am the evidence synthesis
Coordinator at the University
Libraries at Virginia Tech.
Thanks so much for joining us today.
We're really excited to talk
about open access and evidence synthesis.
If you'd like to follow along
with the the presentation,
you're welcome to do so at
this tiny URL link.
And I think that Kiri
will probably add that to the chat.
Kiri's going to be monitoring the chats.
If you have any questions, please
enter them into the chat and we'll take
a break between the very
brief presentation overview
and the panel discussion up here in a minute.
So before I jump into it,
I just wanted to give
a quick nod to the fact that
this is Open Access Week.
So this is the first
of several events that will be
hosted over this week on
the topic of Open Access.
So if you are interested in this topic,
we very much encourage you
to check out the other events coming up.
And this is of course linked
in that PowerPoint presentation.
But today, during this session, today,
we're going to focus on the intersection of
evidence synthesis and open access.
So we have a few learning objectives
we hope that you all be able to
leave here and broadly
define evidence synthesis and open access,
if you're not already
familiar with these concepts, and
be familiar with how open access
can benefit the evidence synthesis process.
And then finally, be
familiar with some examples of
evidence synthesis that have involved
open access in some capacity.
With that, we have a
fairly packed agenda where we will,
I will give a brief overview
of these two concepts,
open access and evidence synthesis.
Then moderate a panel discussion
with four experts who
have actually done this work
and can talk about their experiences.
At the end, that will have an opportunity
for the audience too.
Then some questions to the panelists.
And we'll stop just a little bit
early so that you know,
where you can find more support for
evidence synthesis and open access.
So with that, we'll jump into it.
What is Open Access?
We define open access
With Peter Suber's definition.
Open access literature is digital, online,
free of charge and free of
most copyright and licensing restrictions.
So if you've seen this CC BY
license or this OA lock,
open lock symbol,
that is a pretty good sign that you might
be on an open access article or resource.
There are a lot of variations.
And so if you're interested in
learning more about
the Creative Commons licenses,
you can click this link as well.
But the issue that this is trying to
address is we have
a lot of information that's behind paywalls
and this limits our ability
to use and access it.
And so we'll talk a little bit
more about the why's here in a little.
But this is trying to open up
our accessibility of important information.
The next question of what
is evidence synthesis?
Well, we'd like to talk about this in
terms of an anchoring,
in terms of traditional literature reviews,
which is something that
most folks are familiar with.
So you might have done a traditional sort of
review in a class project or maybe as
the beginning of a to set the background for
grant proposal
or some kind of primary research.
It might also be a stand-alone review,
but one of
the distinguishing features between
traditional literature reviews and
evidence synthesis reviews is
the traditional literature review
seldom has a very clear protocol that was set
forth or a way
to decide what gets
included and what doesn't.
In contrast, evidence synthesis is
very structured and rigorous.
So the type of review that we most
often are familiar with
is called systematic review.
This requires the adherence to
very strict set of reporting guidelines.
It starts with a comprehensive search
that is then filtered into
a corpus of relevant information based
on a predefined set of eligibility criteria.
This review requires two reviewers
to review every reference
at two levels of review.
Then relevant references go
through a critical appraisal,
which really just means they're trying to
assess the risk of
bias that each article has.
And then the data
that's important to be synthesized
is systematically extracted from
all of these relevant references.
It is then that you
synthesize it into at least some kind
of qualitative discussion or
possibly if appropriate, and meta-analyses.
A meta-analysis is
the statistical approach to
synthesising several different effect
sizes from several studies.
And so among several other important features
of the corpus that would be
synthesized through a meta-analysis.
They need to be assessing the same
outcome in the same way.
So a meta-analysis should
always be preceded by systematic review,
but a systematic review doesn't
necessarily always have a meta-analysis.
Systematic reviews and meta-analyses
are aiming to answer a specific question.
They are aiming to inform
practice guidelines or policy
and kind of serve as
the best evidence synthesis
of the best available evidence.
Also what we call scoping and mapping them
reviews which answer broader questions.
Like, what does the field of
this particular topic look like?
An example I like to give?
Because these methods do
stem and health sciences,
although they are used in applied
throughout different disciplines.
No limitation.
Examples I like to give is, you know,
what is the outcome of intervention
and intervention of medication
in a specific population?
That would be a systematic review question.
Whereas a scoping review question might be,
what are the potential interventions?
Are the potential medications to address
a specific ailment and specific population.
This is a really high level view.
Dr. Andrew Booth identified in 2009 team,
there are 48 different types of
abuse in seven different review amylase.
And so I'm not going to go
through all of the details.
But overall, there are
some cornerstones of evidence synthesis.
Synthesis tends to be comprehensive
and done in a rigorous manner.
There's also several steps that are
taken to reduce the risk of bias.
So that includes having a team and also doing
those critical appraisal and
also having a protocol in place, right.
So you're not making
decisions as you go along,
but you're kind of adhering to
a protocol that would allow in theory,
for somebody else to replicate your findings,
which brings us to
transparency and replicability.
It's, it's intended that
these kinds of projects are replicable.
And the reason for
that is that these projects tend
to aim to inform
decision-making and our future research.
So why evidence synthesis?
You might have already picked up on some of
these based on the conversation so far,
but it has a really
meaningful contribution to your field.
So since the synthesis
of best evidence through
a comprehensive overview can
help us identify gaps,
trends, direction of future research,
which ultimately can help us to reduce
research waste and
inform policy and decision-making.
But there's also the benefit
that it brings to you as a
professional can help you
to build foundational awareness,
inform your grant applications.
And also these tend to be highly cited,
especially systematic reviews
and meta-analyses.
Cycling back to the open access fees
by open-access.
Well, many folks lack access through if
they're not affiliated with
some institution like Virginia Tech.
So colleagues, especially those
internationally, tax years,
government policymakers and
non-governmental organizations,
might not have access to
the information that an institution would.
We also want to adhere to
the following values.
Knowledge should be available
in order for it to be built upon,
which speaks directly to
the same mission the evidence
synthesis tries to
serve benefit to the offences.
Similarly to evidence synthesis,
if your information is available,
it's more likely to be cited.
And this open mission facilitates
other uses for open resources such as text
and data mining, teaching, replication end.
We're talking about today synthesis.
So without getting into too much detail,
we kind of wanted to just go
over the specific parts of
the process that could
benefit from open access.
So during the planning stage,
it's really important that in evidence
and we're not duplicating efforts.
So you need to identify
an access existing reviews.
These existing reviews may also be related to
a neighboring topic and
be used to guide the process.
Likewise, reporting guidelines are
open access and other types
of support like educational material,
like this, this workshop right here.
So it's important to utilize
these tons of resources
to help frame your own approach.
Something that you may have already thought.
The comprehensive search relies
on a lot of different resources.
And so finding material is lot
easier when it's openly available,
especially when we're trying to find
full text material.
And then another aspect is
that we can in evidence synthesis,
computational, applying
computational efficiency
such text and data mining is trending.
And unfortunately with material
that is behind a paywall,
this isn't always as clear cut
and it's easy to accomplish a material
that is open access is also open to undergo
these more advanced computational efficiency
is locating supplemental material.
It's really important for
the appraisal and extraction pieces.
So having
a more robust determination of risk of
bias and
also an easier time extracting the data.
So if you publish,
even if you publish with a vendor,
that's going to charge a fee.
You can also potentially,
depending on the contract that you sign,
you could also have
an open repository for all of
your supplemental material depending
on the limits of the publication,
the journal that it
republishing with originally.
Finally, very importantly,
making your evidence synthesis review
accessible to those who
might not have access through
institutional means, is really important.
Remember, these are intended
to be the final audience,
to be practitioners, policymakers,
and maybe other researchers internationally.
And so it's important to make sure that
your intended audience has
access to your review.
Thought that overview, I
will just check the chat
to make sure we don't have any questions.
And it does not look like we do,
but I just also want to encourage folks,
if you do have questions about anything
I just covered, feel free to ask.
But for time sake,
let's hop into the panel
because we've got
some great folks here that are
going to talk today about about evidence,
simple system, open access.
So it looks like we are reading on
one more panelists will still move forward,
but hopefully Dr. Meghan will also be able
to attend here in a few moments.
But before I get started,
I just wanted to say, we are,
we are going to have each of the panelists
answer five questions
during a moderated discussion.
And that will be followed
by a Q and a from the audience.
So while you're thinking of your questions,
please them in the chats,
cheery will be watching and she
will be taken them all
into another document so that we can
ask them in order that they arrived.
If there's a question that
you have to somebody in particular,
please feel free to note
this in your in your chat.
And yeah, you definitely don't
have to hold onto that your
questions till the end.
By any means.
Each panelist Rob two to three
minutes to answer the questions.
Unless we're a little
late and then we will have
a little bit more time for our panelists.
And then I'll go ahead and introduce.
First panelist is Dr. Sophia.
I mean, quant goggle patina,
the regional consultant on nutrition and
physical activity at
the Pan-American Health Organization.
She's also a graduate from
the human nutrition exercise
and food and exercise department,
Asian and feet apartment averaging attack.
And while he or she was working on
a sloping and systematic review to inform
policy related to healthy dietary guidelines,
reducing obesity and
non-communicable disease risks.
We will also be joined by Dr. Liping Wei,
who is a Professor in Civil and
Environmental Engineering Department
at Virginia Tech,
who were, would be
discussing the state of
the art view on the left,
you alert dynamics,
simulation of asphalt binder.
Our third panelist is Dr. Brown,
who is an Assistant Professor in science
informatics consultant at
the University Libraries at Virginia Tech.
Show me discussing finding what is
inaccessible antimicrobial
resistance language use
among one health domains.
And then our fourth panelist
is Dr. Ryan Stewart,
who's an associate professor at
the School of plant and Environmental
Sciences at Virginia Tech.
And it's going to talk
a little bit about meta-analysis,
what we talked about when
we talk about soil home.
So with that, I will stop
sharing my screen and ask
participants to share
their video so that we can see you.
And thank you all so much
for joining us today.
So if the and
then the other thing I just
want to mention is if
at any point you need me
to repeat anything or
or pause or anything
like that to the panelists,
please let me know.
And I did mention
the specific the specific articles
that we had originally reached out about.
But if you have
another evidence synthesis article that you'd
like to talk about that you
think would be relevant here.
Please don't feel limited by any means.
Okay.
So for that, I'll go ahead
and I will start with our first question.
So Dr. Latino, If you could go first,
please describe your field of research,
including a little bit
about your experience with
evidence synthesis and
her recent evidence synthesis publication.
Hi, thank you so much for inviting me
and to respond to your question.
My field of research
is public health nutrition,
specifically on food and nutrition policies
that aim to create healthy food environments.
So nowadays in the policy-making process,
there's like
an evidence-based policy approach.
And this approach is
being used more and more.
So this approach is like
an idea in the bullet policy,
proposing to use research,
findings and policy decisions to
inform new policies or improve
the ones that are already in place.
So therefore,
all the evidence synthesis is very common in,
in my field and it is
an excellent way to present that.
And the present research to the policymakers.
Because we all know that policymakers,
they usually have like
a very small amount of time.
To hear about and to take decision.
So this is a very well-resourced be used.
And on regards my experience, yes,
I do have experience doing
a couple of evidence syntheses,
but the last one that I abolished,
it was the one that goes
that a told you about.
So I use evidence synthesis as part of
my PhD preliminary, preliminary examination,
where I conducted a scoping review,
the examined the influence of
restaurant menu labeling policies
on product formulation and re-using
the serving size of menu items,
not just in the States but globally.
Dr. Brown.
Yes, higher buddy,
happy to be here and thanks for
the invitation because at time and Brown,
I'm an assistant professor here at
university libraries where I
also serve as the science
informatics consultant.
And what's that really entails is I
work with faculty and staff and
students all over campus where I integrate
computational bioinformatics techniques into
their research and teaching for
whatever ways we can have more impact and
really meld those computational
experimental world, worlds together.
I heard you mentioned or
someone mentioned MD simulations.
I do that too with was another person.
So there's a lot of synergy here in this.
And so with that
and being able to kinda bridge between
the sciences and in big data in
a way and work
with students to help us do that.
We had a group of individual approach us from
the biological systems
engineering department where
they were working to figure out
how they could answer this question
about improving language use
amongst are many constituents
of individuals in
this One Health Consortium
that they were a part of.
They identified that people
were working on similar things,
but we don't know about them and
things like, and things like that.
And so we worked with them to
develop kind of a first pass method of using
evidence synthesis to screen
and download and do
text data mining on
different open access papers
related to antimicrobial resistance,
which is a problem on the horizon for us.
And we have a lot of different domains
that work and antimicrobial resistance.
So the environment, animal and human,
which are the domains of One Health as well.
And how we talk about
that is not really consistent.
So what we're using in our keywords,
what we're using in our abstracts
and stuff like that to get these things
to the top hits and
the things that we're looking at.
And so that's kinda where our project
came about of figuring out how we
could get this and use evidence synthesis
with these collaborators.
And then also kind of
realized all the people in the room and
myself included who does
antimicrobial stuff
in a whole different world.
Chemistry language, for example.
See how we're all
talking about this in real life.
It kinda breaks the boundaries than 750 pay
really makes for a scene
and make inferences against you.
It's been a teacher numeric thing.
Thank you. Steering.
Alright.
Thank you because I
feel it bounced side. It's great to be here.
Excited.
So yeah,
I'm Brian Stewart and I'm in the School of
plant and Environmental Sciences
in my field of research,
it's very broadly Soil Science and hydrology.
And so within that we work on
different problems,
kind of how we can manage soils to improve
water quality and
environmental sustainability.
And things like reducing
pesticide transport or trying to measure
greenhouse gas emissions from
soils and understand what are some of
the dynamics on bird
that's even have a student working in
vineyards and viticulture
trying to better understand
how soil properties effects
wine great quality.
So, and we're kinda all over the place,
but one of the projects,
so one of the areas that
I've really focused in on it,
It's called soil health.
And it's kind of this idea of being
analogous to human health.
How can we understand how
our management practices or
even the soil properties
himself translate into
actual healthy soils
versus non-healthy soils.
And so when I first started at Virginia Tech,
I was fortunate to get a project
funded by the Natural
Resources Conservation Service.
Or we set out to try to better quantify
soil health by looking
at what measurements made sense,
how to interpret it, things like that.
And the analogy that
we like is it's kind of similar.
We went to the doctor and ordered
up a bunch of lab tests.
Do you need somebody that is able
to interpret them and tell you what
that actually means for you and
your lifestyle choices in
your diet and all these things.
So that's similarly
what we were trying to do here.
But in the realm of soil health.
And it's great to hear from you all about B.
It was to hear about the,
the overlap and
differences between what you're
doing and how
evidence synthesis has played a role.
And so with that in mind,
my next question is,
why did you choose an evidence
synthesis method for this project?
And we'll start with Dr. Brown.
Yes. So we really started going about
the evidence synthesis route because we
needed to take information from three,
at least three different domains to
at least represent one held.
So environment, animal and human.
And from that, we really, you know, I'm, I'm,
none of us were experts in any of these
no domains necessarily comprehensively.
And so we wanted to be able to make
decisions on what were
the most important themes,
keywords, et cetera,
as based on those domains.
In addition to the overarching domain
of One Health as well.
And so having those kinds of
camps of information that we needed
to be able to bin it things
into been different kinds of papers into,
while also trying to see
trends at a higher level,
kind of seem to be the best,
the best approach for that.
And we also needed to do this
for a large level
of information because we
needed to do this as a
systematically as possible and
make sure that we're being
no sampling as best we could these areas
and not kind of biasing
our sampling or our identification of
keywords to any one of
our four categories that
we had in the long run.
And so that is kind of the route
we took with that and why we made that.
We also needed to
consider we need at a large,
like a very large amount
of information of all the,
all the papers within
a timeframe that we could get and then
have random samples from
it and go about that route.
And so that was that was how we got
started on the route that we ended up taking.
Stuff.
Yes.
So like I said,
we have this project's been with us how to
quantify it, soil health.
And so during that process,
we've gone to the literature,
looked at some different methods,
things we know how to do.
It seemed like they were and put
together what seemed
like a comprehensive list.
But then, you know,
there's a lot of other people
working in this area.
And so you go to
conferences and start talking to people.
It's like, okay, these things are the
same and these are differnent.
And just got me kind of questioning why.
Why are you making these choices?
Why did we make these choices?
And what are other people doing?
Same time, I had some more senior colleagues.
So I've been doing this stuff for
20 years or 40 years.
You should be looking back at
what we're doing to
so rather than just reinventing the wheel,
you should be yeah,
just cognisant of what we
did wrong turns to be made.
That so I just got
me kind of thinking like, well,
has anybody actually done a survey
of what methods are
being used for assessing soil health?
How many different indicators are they?
How can they be Groot?
And the kind of at the same time,
there's a non-profit entity called
the Soil Health Institute that was coming
along and they were starting to
try to standardize some of
these these methodologies
and make recommendations.
So it seemed like
the right time to do a survey of
the existing literature in
this realm and see what were people doing.
And then from there,
extract some of that data
out and actually try to do
a meta-analysis to say what seems like it
actually works for a specific question,
how to do its cover crop?
Yeah.
And I mean, you started your process.
It sounds like actually with
the personal contact kind
of approach where you,
you know, folks in
the fields were doing that work.
And that's, that's a really important step
in evidence synthesis as well.
That's not always apply it.
And so it's very cool. Dr. Patching them.
Sure.
So first of all,
I chose us groping review
because the nature of these research methods.
So this is a method to map,
describe, and provide an overview
of the published literature.
So when I decided to do this is because
am a lot of countries
were implementing them menu labeling policy.
So this is a policy that you can go get
the calories that each item
in any fast food restaurant has, right?
So I start looking
at the evidence and it was very confusing,
but because there were a lot of
published papers that say
that there was a reduction in galleries.
And some of them they were
saying yes and ALT others
like our formulation in
the products which is good.
But so it wasn't very clear.
And like my research and part
of my PhD and above it,
if it was like to guide and
assess the policymakers yes.
Attitude to take this route and
to conduct a scoping review
to try to fill that gap and to
describe what's here and like what is needed.
So that's why I did it.
And also because as I said before,
it was part of my PhD,
I didn't have any funds.
It wasn't part of a like
any like research project.
So these are research method
that do not need many resources.
But if it doesn't,
they need a lot of time.
So basically at the end it was myself
and my time and
my computer so that make it very feasible.
Your project is such a great example
of evidence synthesis in general,
because the scoping review method, right,
was intended to act as
the precursor to the systematic review,
right?
And so you, you had that opportunity
to illustrate how well that
worked out for our next question.
And we'll have Dr. Stewart start with Beslan.
How difficult was it to find literature,
datasets and or
other resources for your review?
Yet so I mentioned the Salton Sea as
being this entity that was kind
of being developed and then getting there.
Along the same timeline.
And one of the things they start off with
creating what they call it
the research landscape tool.
Where they were going out and creating almost
like bibliographies of relevant materials.
And they're pretty broad, but they
included theses and dissertations,
white papers along with
the peer reviewed literature.
And then they organized it.
From, here are the problems,
here are the indicators and
ways that you can measure it
and here are the outcomes.
So that was a nice kind of framing tool.
And so we started with
that tool and just select
that were two questions.
One related to tillage.
One really had to practice
called cover cropping.
And went there and said, Okay here all the
resources listed under these two practices.
And then from there dove in and found
the peer reviewed
literature that they compile.
So they did the first screening for us
in this particular project,
we've done other meta-analyses
where we've gone
the Web of Science route and lucky
for ISI and doing keywords.
But I guess this
was unique in a sense that somebody
else had done the initial screening
and we worked from there.
The reference.
And it just dependent some articles,
Obviously we had library subscriptions
or the articles were already open access.
Others we had to go
through the interlibrary loan
or email the author
trying to get copies of it that way.
So I think for this particular paper,
we had something like
200 papers that we had gotten.
So there's definitely my post-doc
spent a couple months just getting
the references in hand
and organize that number and all that.
So state goes big left associative
that Dr.
Peggy knows that was made.
And so these particular paper,
it wasn't that hard.
But that was because this wasn't
my first experience
with that evidence syntheses.
So I didn't talk about
like one before that when it was
a nightmare because if you don't get like
a good research question
or if you are not defined that
the mesh terms that you're going to look
at in the pointed databases.
Like you can spend months
and months and months researching,
researching, having different results
without like datapath.
So I think that the tweak of
any evidence synthesis is to spend
enough time to develop
a good research question.
And with a research question that
has the population or object of study,
the exposure and outcome and the timeframe.
Then you can define
your mesh terms and even your, your,
your criteria that the selection criteria.
So with that very clear,
it was very easy.
So as I said, I did it in for
my preliminary exam as a PhD student.
So I spent like
less than two months
from the date that I started on,
like the paper was done.
But it was like two months
that I was just doing that.
Like I was just focusing on that.
So he's not that simple.
But if you have a good research question,
I believe that it is not that hard.
Dr. Brown.
Yes.
I can is saying and saying
our mesh terms and getting
our search terms as
defined and as comprehensive
as soon as possible.
And that was working with
another librarian here in
the university libraries was
absolutely essential for us.
So we had a little bit
of a different approach
where we had to go very broad and
make sure that we got enough sample size
of papers from these different domains.
And so making sure
that we had our search terms as
accurate as possible and
as kind of encompassing,
not even thinking about phrases
we wouldn't consider. So environment.
We didn't think about water and
different kinds of soil words
that should be in there as well.
Because what's going to hit, you know,
not not just the word environment
or something like that.
And so we needed to make sure those were
included so that I
can wholly agree with that as well.
On the other side, for us in terms of finding
literature and being able
to access the literature.
We wanted to also make
our process of doing that the,
the text and mining
and natural language processing that
we did on these papers in order to
start to see trends reproducible.
And so that meant we needed
to be able to access
papers and make sure other people
could access papers as well.
So we used a program
that only let us originally download,
search, and gather
open access papers as well.
And so that was
something that was important to us.
We then we did do a secondary Nano a set
so that we could have
included that in the paper
because obviously we only had OA,
it would have been the most
potentially lead to some bias as well.
So we did a smaller set,
but we had to again
work with our librarians to make sure that
we could act adequately
download that information,
download what we needed in order
to do the text data mining and
natural language processing on that to find
the trends of which
we were starting to observe.
So that is a really
key question there I think
in this whole domain is how and what is open,
why it's important as well,
and where it can really
lead to in the future in
terms of being able to parse
this information out.
For individuals, no matter
what domain you're in.
But then also being able to
reproduce some of this work
as well as the big thing,
we always should be careful
about that as well.
So those are those are
some insights that we got
from that Dr. Brown,
you have kind of different spin on
this whole conversation to
the application of text and data mining,
which I only mentioned
briefly in the presentation.
But it's definitely
something that, I mean, you know,
I've talked off off camera
on many times and it's
definitely quite a challenge
that can be addressed
through it In part here.
So we will return to Dr. between to
ask what role did open
access planar excuse me.
What role that open access play in
your review and why did you
incorporate of Nexus in the sentence?
So I personally believe that
open access has a lot of advantages.
I know that there's a big discussion out
there and we should use open access or not.
But especially for me as a young
professional or a junior researcher.
I think that this is
an amazing opportunity because
open-access increase visibility of
the research by giving access to everyone.
So right now I'm
starting to build my name and I can reuse
though a like not
being that well known in my field,
but people can have access to my research.
So I believe that, that's a very,
a good thing about open access.
And for example,
the scoping review that
like I was talking about,
was published over a year ago,
like you're on May of 2020.
And right now has 2478 abstract views,
over than a thousand full text views
and 11 citations.
And I, I'm like,
I feel really believe that this happened
because it was Polish in
an open access journal. Dr. Brown.
And I promise I forgot to look at what
the next question was when I
when I started my previous answer.
But I can I can continue to follow that up.
So it was absolutely essential for us
in terms of the review
and why we incorporated it.
Like I mentioned previously,
it really gave us
a scope of information that was as broad as
possible in dealt with
the reproducibility of
the text data mining that we were doing,
which was, was important for us.
Last pieces we actually then
our paper is open access as well.
I guess that would
have been had hypocritical.
We did not make it open
access after we did all that work.
Because again, the, the
biggest hurdle that we were seeing
was how slight changes in
word usage greatly impacted the,
the, the top hits of
papers for these different domains.
I mean something as basic,
or at least it seems basic me,
but it's not basic to others is
antibacterial resistance
versus antimicrobial resistance.
Really in the same areas
right there or just the how we
abbreviated though some
individuals abbreviate
these things at AMR, ABR or AR.
So being able to
know and scope that and make suggestions
for how we can add some commonality
in our language and then
making sure our findings
and suggestions of that.
We're also open access
helps to land not towards the problem of
people not knowing our being
able to find this information
readily and have access to it
without pay walls or barriers.
And so that's why
we wanted to do that
was the whole point of the work
in the first place is to enhance
the language that we
have here and how we use it.
So that more strategies to combat
antimicrobial resistance
can be cross-disciplinary as well.
So that, that's how
we've incorporated open access.
The last piece I'll ads,
is it actually using
open access for our data set,
for TDM, for this and made it easier for us.
Because we did not have to go through
a variety of different kinds
of APIs and things like that.
We were able to just utilize it in mass with
one program we're doing rather than have to
find based on publisher,
based on a variety of things,
how we could get access to
the volume of literature
that we needed to be able to search it.
Thank you. Dr. Stewart?
Yes. So even though
some of the references were not open,
honestly, we did want
to have that information available.
So the postdoc who really
lead some of these efforts is
background was in database,
database development and database management.
So he spent a lot
of effort actually compiling the data that
we extracted into a spreadsheet base form,
but organized in such a way
that future people could
go back and easily extract the data,
can be analyzed it or
use it for cancer, other questions.
And so this, this particular paper is kind of
its first product of that effort,
but we did several others beyond that.
And SES time you can tell.
To add to it.
So there's a lot of yes,
some of the automation sounds
great because there was a lot of
manually pulling data out
of figures and things like that.
Then along with that, but that's
not a database is managed on
a GitHub where anybody can
go download the database,
even make changes and
suggestions and using version control,
we envision this as more of
a community resource that people could be.
Uploading their own data is eventually.
So that's the vision
hasn't necessarily translated glad yet.
But the paper itself
we published in
an open access journal that was
fairly new and that kinda
soils and agronomy realm.
But I think it was a impactful paper.
At this 0.1 of them are highly
cited once in that particular journal.
And I think I'm being open access
played a role that
anybody around the world that's
working on this can easily find that.
Just look on Google Scholar
and actually goes to that
the V tech works version
that I or somebody
else must have uploaded on the way SIADH it,
go dig to actually get to
the publisher's version of it.
But yes, I think it was
just makes it easy, makes it,
I can share it freely
at the same time without
worrying about copyright restrictions
or anything like that.
Pan. There's just no paywall story about so
anybody can go can go out there, get it.
So that was one of the things I really
wanted to, if possible,
publish this as an open access article
just to get that broad readership
I met this guy,
were able to find the right venue for it.
Right around. You'd like to ask a question.
What I have, I had another point that I
remembered as a CEO who's talking,
I thought we could not have
published open access without
the support of the university libraries
to mention fun eyes on.
I'm sure that's also known out there
to the group that pretty
much allowed us to
public publish open access as well.
So kudos and highlights to that for
making that a easy process
for us to be able to do
and for us to maintain
kind of our ultimate goal
for getting our work out there.
So definitely wanna make
sure everybody knows about that.
That's fantastic.
And I don't trust you anymore saying
that you didn't look ahead at the questions?
No, the perfect needed the perfect lead
into the left unstructured
question that we had.
So so Dr. Brown,
if you'd like to start this one off,
did you include open access funding in
your grant proposal or get
funding for a publishing in another way.
And if not, will you consider open,
including open access funding
in your grant proposal going forward?
So you've already started
to answer a little bit,
so yes, one.
I definitely see that it's
not looking at the Goodbye.
But anyways, no, I really
want to emphasize this just in
general because I usually
wasn't one to think about
publication charges all the time.
I shoestring, making sure in
the grants them some money
that I'm making sure personnel
are covered and things like that,
but just a few,
like $2 thousand or
something like that will get you
pretty much publication open
access in any of the PLOS journals series.
And those are great then used in
a variety of others as well.
And that can be such a big help
in terms of getting your work
out there and getting access to
the posted on Twitter or things like that.
It really can have worldwide
coverage at that point in time.
And the other thing that's really
important there to think about too
is as well teaching as well.
The more information of
this great research that
we're all doing here at
Virginia Tech and get into
the hands of students as well
without pay walls at different
institutions and things like that.
The better it is just in general.
And so that's huge
for that, but we're also lucky.
So the project that we worked on,
the anti-microbial resistance one
was not grant funded,
it was a collaboration and a,
an effort amongst a handful of
research researchers here at
Virginia Tech and at other institutions.
And so we really, we wanted to do this.
I think there might have been maybe like
a couple $100 from
from one of the other institutions
that they could contribute.
I believe they did contribute.
We really had the support
of the suspension fun,
which was able to split kinda
the the amounts amongst myself
and other Virginia Tech researchers.
There's a I'm probably not
the best person to tell
you all the details of this.
Please see the link that
Curie posted in the chat.
But you pretty much have
a cat per year instance,
there were multiple BCCI faculty on this.
We're able to kind of split that
amount amongst us so
our Cap isn't inflated in any way.
We can keep publishing open access and it's
a very generous cap to begin with.
And so we really utilize that.
And I highly suggest everyone to look into
that and contact individuals
that run that to,
to make the most out of it because
it's incredibly
important for our work to get out there.
Or if not, that if you want
to not be able to publish open access,
maybe it's too expensive
and there are some journals where it
is unfortunately really expensive.
You can also do preprints and use
preprint servers and use VGB tech works here,
which is the Virginia
Tech universities libraries repository.
For that, the kind of
preprint version of the work
that you are publishing.
So all those options are super,
super great to pursue and anyone
in libraries can also help with that.
A really great point. Thank you.
Yes, So we also use the open access,
the pension fund for this work.
So that's a really great resource
as Dr. Brown said.
Yeah, just makes these things
possible versus trying to scrounge up
$1500 out of, out of the research dollars.
So on the question
of putting open access money into grants,
I mean, I try to put 500,
$1000 or whatever into into a
grand It's just yes.
Students type and then travel on Gerald.
Just with these federal grants,
state grants, Cathy,
they tend to be CAC so it's just hard,
squeeze everything in so it doesn't
end up being necessarily enough to
pay for a nature
journal or something like that.
But we try to
have a little bit in there and and
not dip into it and use that
to to help support that.
But as Dr. Brown,
so there's a lot of really reputable,
high-quality open access journals that are in
that 1500 and 2500 range
so that the open access,
sufficient funding gets you
a lot of the way. There is.
Just a matter of coming up
if there's if you're a little bit sure,
How do you, how do you pay
for that? Like that.
But I think it's useful,
it's definitely in
that default to turn audiences
rights that I think
to try to try to stretch and make it happen.
Dr. patina?
Yes.
So as Dr. Brown and Dr. Stewart,
I also received funding from
the OpenSSL advection fog
from Virginia effects university libraries.
And basically the library
be the article processing fees.
And both of them said,
it's a very easy process.
All of that of that personal that it works.
This part of the unit,
they University library,
they're very nice and they're
always willing to help
with any question that you have.
And P 500 consider
including open access funding
in any grant proposal?
Yes, I I will strongly encourage to
incorporate funding for
open access publication.
Despite there's any funds available
as open access salvation
that bridging ethics class,
or even if there are other opportunities,
I believe that it is very
important to give visibility to
the research
that he bullish and
openness disease that might make you learn.
Excellent.
Well, thank you-all so much
for your time so far.
We are have plenty of time for Q and a.
So we'll go into that section now.
I will pull up the questions
that we've been documenting that
curates and also encourage audience members.
If you have an allergy question
yet, please feel free to.
So it looks like we have
one question come up.
And that was true.
It's also going to add to the chat.
I was wondering, is there a pre
required work that we need?
Excuse me.
I'm sorry? Is there a clear required work we
do have before making
a decision of conducting synthesis,
synthesis review, such as checking
if there's available documents
that will support us.
So I can I can briefly speak to this.
There are reporting
guidelines that are available.
Prisma is the one that we reference most
often and I think we can probably
get that into the chat as well.
One of the first steps that we recommend is
to make sure that you
review hasn't already been done.
And so I kind of reference that
earlier, but again,
when reviews are made open,
it makes it a little bit easier for
folks to have access to that.
And had mentioned the pre-print situation.
And so having, you know, another,
another related,
totally, not totally related,
but the idea of registering your protocol
before you actually finish your
study is important as well.
And so by registering,
you are allowing others to
know that your work is underway.
So I will also ask if anybody would like to
comment on making that decision to,
to do an evidence
synthesis review in the first place?
I might not comment on that exactly,
but how you mentioned that
pre-registration codes that OK.
Framework is an awesome place to do that.
I've not done one.
We have an Open Science Framework
for our paper.
That is the one that I'm good.
I've been talking about and
we we didn't pre-register with that,
but we did use it to upload our scripts in
our data analysis that we
did and also have that available.
And I also, I know at times like you can get
there's different kinds of applications you
can do for pre-read gestation
and things like that.
But what it's really cool is it's kind of
like letting you lock in
a hypothesis and see how it
goes and then being
able to, to go from there.
And I think that's important in science
because sometimes the bill not,
not super exciting results
are still results that need to be out there.
And so that's a really nice consideration.
But I can highly recommend
using Open Science Framework.
I use it more for kind of like
a gatekeeping place for all of our groups,
scripts and things that
we need tutorials that we teach.
So if anyone ever asks us,
I could say all that's available
here on our OSF for
methodologies that we use
or things like that when we say we did it,
used
in-house analysis or something like that.
So I really like how it's organized.
It has a DOI and
a citation for it for the OSF.
So I highly recommend
using a mat as well for,
for obviously evidence synthesis,
but also just other research projects
you might be working on in general.
And I think both Dr. obtain a darker
brown talked about having the right question.
Again, The question I had,
I think that's would fall under this
just so you an example,
we did a meta-analysis on how cover
cropping practices
affected soil organic carbon.
And there had been a couple of
reviews and meta-analyses on there,
but it was more getting into, okay,
they focused on
a specific geographical region
or a specific cropping system.
And so we're able to cane
or state our question a
way that it was a new analysis.
And actually one of the cases,
the authors of that other analysis
send us their data, they idiots,
we're able to ingest it
into our own analysis
and then extend it beyond.
I was very helpful stuff.
And I just will add.
So in order to add any evidence,
seeing synthetase is when you
are not sure about
the evidence that is out there.
But you already started somehow the research.
That's the perfect like
excuse to start a line.
But it doesn't guarantee that
you can do it because
maybe when you decide to do it,
then you'll find a bunch
of other synthase is review.
But actually, that's
an excellent way to start.
Like if you are curious and literature is
not there and it is not clear. Go ahead.
That's the first we'd like.
That's such a good point
as well because I know a lot of
folks are hesitant to
get started with evidence synthesis,
thinking Why haven't really
seen much out there?
But identifying gaps is
very meaningful to the field.
Well, I'll also open up
the opportunity if any panelists wanted
to ask questions either to each other
or also back to the audience.
That is definitely welcome.
And if not, I have a few other questions,
but I came up with while who'd been
talking because your projects
are very, very interesting.
But maybe I have a question for Dr. Brown
mentioned automated data extraction.
Could you even how you got started there,
what that looks like, what's the QA?
Qc?
Yeah. So a variety of
different packages in Python
that we utilize for text data mining.
And we used a program called Content Mine,
which is out of the UK.
And it actually, it
creates JSON files that are
parsable for keywords and for
binning and for frequency analysis.
For us to start seeing
potential trends and able
to drop words and things like that.
And so we utilize that as a program.
And then from there, pandas
and Python to start actually starting
to do some the TDM stuff with
the scikit learn and things like
that where within those packages.
So that was kinda the route that we took.
We were we were very high level
with what we worked on.
I'm sure a lot more could
be done in this area.
But we kinda just wanted to see in
general trends of language usage,
especially with keywords in abstracts.
And then as it represented the overall work.
And that's, that's where we focused
in and some Python and,
and mining of that in
frequency interactions
and maps and stuff like that.
And network analysis was what we did.
But we couldn't have got it, got
it into that JSON format
that we needed to be more readily parts
without content mine.
And that also let us utilize
the really great search terms
that are librarian that we
worked with gave us to then download based on
that to a local computer
so we can actually work with the files,
not have to do anything too laborious
their eye and also share my experience.
I didn't they did that automatic,
but I did use that Coby than software.
I still I'm not sure if
you're familiar with it,
but it was a tool that
actually the librarian that I
reach out in Virginia that does this is this.
Scoping review.
She introduced me to the software
any grade because it's
a very useful tool to organize
all your evidence and also even to to,
to process your selection criteria.
So at the end, you just
upload the reference as using
like at node or SAP data
or that reference manager
that you're using at it.
It's very easy to
screen and to save the data there.
So Dr. steric, you,
you mentioned be emailing authors
and building upon research authority
that had been shared with you.
And so I wanted to just ask
you a little bit about that experience,
about how successful it was to reach
out to folks and get there
maybe unpublished research or data.
Raw data?
Yeah.
In general, I found that if you
e-mail on out there,
they typically are very
happy to share their research.
So it's, I think if we didn't hear back is by
an indication that the person's
just really busy and not keeping up
with e-mail versus a lack of interest.
I don't think anybody Yeah.
And if you're going
to use their data insight,
their work usually that's a wins for,
for everybody on
the people who shared their data.
I think it took them
a little while to get back to us,
but yeah, there was no real strings,
we acknowledge them and
paper acknowledgements,
but there was no authorship expectation
or anything like that.
And it just yeah,
I've had to go
through the organization system,
make sure it makes sense, check the data,
quality control against
the original publications,
but it didn't make it
easier and that there was,
Remember how many, you know,
a few 100 data points
that we were able to get from
that and not have to go extract them
from the primary sources directly so
that they seemed like
they were totally okay with it
as long as we acknowledge them
and cited them, of course.
And that seemed to work out.
Did you did you identify them?
Was the only articles
that you had already processed
in and within the corpus or did you reach
out to many experts in
the field, at least terms.
So, well,
I guess one thing is when we did our search,
literature says finding PDFs
of all the papers.
So some of it, you couldn't
find it Through that.
The usual channels we
reach out to the authors and try to get it
that way or reach out through
the ResearchGate or whatever
to try to get a copy.
The data specifically with
somebody who had already published
a meta-analysis on kind of a similar topic.
They just look debts. This is visited
or they're looking at
the pompous reason of our two Ts.
So they've done a meta-analysis,
but it's just focus on this one,
region and discipline cropping system.
Whereas we wanted to do
analysis at a global scale.
So we're able to take their specific data and
feed into this larger
analysis they were doing,
what do your cropping systems
across the planet.
So that made it nice that it in an
extra five or 10% of our total data set.
But it was just able to get that all from
one in this course and untreated into there.
Compare how our results
compared and contrasted with what they towns,
but that specific region as well.
And it's really meaningful illustration,
it's only five to 10 percent
of your overall data set.
It's important.
So plays a really big role.
Yes.
So another thing that I wanted to
ask the panelists is we've
talked a lot about
the positive aspects of open access.
Can you think of any barriers, difficulties,
lessons learned,
or words of wisdom
to share with the audience.
I mean, I don't want to hog the time,
but I saw that period put
in the limitations on
the open access a pension fund.
And so a lot of the journals
that we typically think
of publishing and have hybrid options.
So you can pay to
have your article made open access,
but it's still a subscription-based
model for at least some of them.
So that doesn't qualify
for the open access suspension find.
And so it's it's a challenge.
If we're relying on particular
resource to help pay for it,
Can we find a journal that's
suitable equivalent?
It's going to have the same readership
is going out, same focus.
And so their husbands in town.
So clearly one we're kind
of trying to work on as a systematic review
where one of the stipulations
from one of the collaborators
was they wanted to publish in
an open access journal.
And so she's finding that
the right journal in terms
of the rigor of the process,
the audience, who's, who's supporting it.
I mean, there's a few candidates,
but it quickly you start at
400 open access journals and you get
to about four pretty quick.
And some of these cases.
I was going to say the exact same thing.
So yes, you do need to be careful there.
It's frustrating to do
that and deal with that sometimes,
but I agree with everything.
Dr. Stewart, you said.
Well, I'm thinking up in
another limitation is that there's a lot of
discussion around if open next
is they are doing it for
business or academic purposes.
So sometimes back because
they charged the sum around,
they are there suddenly beta there.
I'd like these qualifying some journals.
So it is very,
very important to select
your journal to know and be sure that
the peer review process going
it's supposed to be and they're
not trying to make profit.
But that is easy to
do any of you in
defining that factor of pitcher.
And that would be a way to pull
those that another maybe
kind of building on that.
He'd done some workshops and
stuff and other parts of the world.
And they're very interested
slash scared about predatory journals.
And I think it's very hard for
some of them to know what is open
access versus what is predatory.
And so we're going to talk
about things like is there peer review?
Are they, are they just soliciting
anything from you?
What does it look like?
Or you choose the journal
as a journalist, you see?
But it's certainly can get kind of in
a gray area with some of
that open access journals.
Are they? What's their motivation?
And again, what's the audience?
I think it's a good question. Is, are
people reading this journal?
Are they citing it?
Are they using it?
Or is it just be published
and somebody's make an autumn I
ask that the research is
not having much value on that.
Yeah, that's very good point you bring up.
And I just want to share
the directory of
open access journals. I believe.
Oh, it didn't. It is a repository.
So if you're ever in
doubt or you're looking
for an open access journal.
Welcome to check out that site as long.
So I'll pause just for a little bit,
see if there's any other questions
or any added that
it can really be tricky to
find the right journal.
So to reach out
and consider thing, checksum it or
Well, Judy Garland, huh?
I'm not super involved in today,
but I just want to jump in
and say thank you all so much for
sharing your experience with
great to hear about
real life experiences with
evidence and business and open access.
And since it's open access week and
Curia put like all the links in chat.
Maybe it's also an opportunity
to point out the new open access policy.
We have that tag which isn't thus the humans
having your publication in
an open access journal.
But if you can't, can't do that.
It is also a great option
to get your work
out there and an open-access fashion.
So I think she already added the link in chat
and definitely let any of
us know if we can help out with that.
And also just to highlight,
we did talk a bit about
B opens prevention fund.
That is going to also be one of the topics
that is discussed at during
a WE DO during a week.
So we'll make sure i'll I'll
share that here in a minute.
So thank you all so much.
Thank you to our panelists,
Dr. Bettina, Dr. Brown, and Dr. Stewart.
This has been very
informative and it's been great
learning about all of your research.
Thanks for having us because
it Thank you very much. Absolutely.
So while we're wrapping up,
I just want to share, you know, if you're,
if you're looking for support and
evidence synthesis or in
open access, we are here.
This is not by far
all of the people at the library,
so you can help by,
we are all invested in these kinds of
initiatives and please feel
free to reach out to us.
So top layer evidence synthesis,
the poor and the non-human got folks who
focus on open access.
Felt young is, is the Virginia Tech
or B tech works manager, repository manager.
And and it's focused
on research Open Access mostly.
And then Anita Walz is more on
the educational resource,
open access material.
And then I had another shout out.
There are a lot of events that
are hosted throughout the semester.
Got the year for open access.
So like var even talking about this
isn't first session of Open Access week.
And I will just scroll down to share and to
highlight the pension fund
of that will be on Tuesday a TPM.
So that is something that's
interesting to you and you're,
and you're looking for funding for
publishing your own open access article.
I'll please do consider signing up.
And I'll also add that evidence
synthesis hosts series of workshops.
We have one more this fall
on critical appraisal,
but we also post all of our video recordings,
including this one will be posted as
well on our library guide page.
If there's ever a workshop that you are
interested in learning more about,
please do reach out to us.
And then finally, we'll
ask that before you head out,
you share your feedback.
We are actively trying to
improve the session that and learn
from areas that were
successful and areas that
maybe we can add ons you.
Thank you again so much for joining us today.
And be in touch.
Go ahead and stop the recording.