>> Okay -- thank you for the chance to give you all an update on the catalog and the recent
developments that we have a moment of but we thought we would originally commuted some
of these develop it to you in a slide in Eric's director report that we thought Council might
be adjusted in a more detailed report and before server presentation I would really
like to think Helen is group at the bio informatics substituted EDI who have done a lot -- is
-- think we may have one or two key members [ Indiscernible ]
>> Okay. So by now most of us are familiar with his view of the catalog that shows the
different to type [ Indiscernible ] that have been identified -- we think this type of diagram
every quarter -- today I thought I would take you -- let's see -- but I would take you behind
the scenes. >> And show you a little bit about alteration
workflow as well as the other recent develop its related to developing oncology as well
as the diagram. >> And finally I will give you a preview of
our new automated diagram. >> To give you a sense of how information
flows into and out of the catalog, we have a weekly literature search and we survey the
NIH service for eligible studies. We then we look at these eligible studies with our
curators for everything the table, everything a page of the paper to identify eligible [ Indiscernible
]. >> We have first level duration that extracts
study level and grade level Association we think is important for a second level check
-- both for quality and consistency purposes. So we also want that level of checking the
before we publish the data, we have him committed a data full process with colleagues at its
EDI whereby they provide some additional vacation and additional [ Indiscernible ] -- and finally
the data are published in a web. >> So before -- we have a quarterly diagram
just done by hand by [ Indiscernible ] so every quarter when the Associates and she
added they work together to literally can't place each new. On the diagram.
>> So as part of our ongoing secure improvements -- one thing we're working on now is developing
a framework to more consistently and I expanded way click standard information on the creation
side of things but it is worth noting that everything you see here in red is by and large
all manual -- it is very time intensive and of course there are some ways in which we
hope that we will be able to increase our efficiency of duration through informatics
and other development and of course the clever readers at EDI are working on a number of
developments for ecology apology features -- the focus of today's topic our features.
>> So some historical perspective -- many of you may be interested in knowing that before
the catalog with database was preceded by an Excel spreadsheet -- datasheet and before
they were table but this is why you see the word -- table.
>> Appear. So we now have a web entry that was developed by the NHI web team -- this
is the front page of the curator feet if they want to start duration or into the study or
check on the status or posting or so forth to
>> This is just a brief subset of the data we collect -- RCC here potentially is a piece
of information that the curator manually enters in a case may seem a little bit of time -- but
it is by and large manually entered. >> We did with the help of our operators at
the functionality to where the data are in a spreadsheet they can be uploaded directly
into the database which has been helpful in terms of reducing errors as well as having
-- the paper in the more time efficient way but
>> We do monitor the most popular purchase that our -- performed by our users -- so here
you see on the left the most popular terms that were searched for in the calendar year
to date. And for the visual -- this is a word portal information where the size of -- is
proportional to the number of searches. And you can see here that the most common searches
are those related to various cancers and diabetes and to lesser extent some other common diseases.
>> So this is for those of you that use the catalog -- this is a snapshot of the interface
-- a user can search in this link box for a particular strength that matches a trait
in the catalog. Or you can browse this relatively long list of the diseases you're interested
in. And that will break the relevant salt in the catalog.
>> And so Helen Parkinson who is a effort in developing and adapting EDI noticed that
of course this is a relatively unstructured trait list -- were simply can see that a trait
such as diabetes is if you look on that long list of traits, is classified both under diabetes,
as well as a type of diabetes -- perhaps with other traits and accommodations with the paper
reported on patch message that opportunity to integrate this page into an existing oncology
and facilitate -- ontology and facilitate traits to be able -- enable a more systematic
for powerful searches. So ontology that we're using here is called the existing ontology
-- Edward facilitates variables such as an on the time ago feature or a particular disease.
So the oncology -- ontology also allows relationships to allow have a parity for wearing fur expanded
disorders. >> Will also allow for common editorial searches
such as that when you see here but >> Be able to broadly categorize things mean
that we can go from about 200 manually traces as we find on the current diagram to the order
of 20 ontology defined traits which of course makes it easier to kind of ruse the guideline
visually while us find treats -- trait. >> Ontology can also be used to improve the
generalization -- categorization as I looted to -- and to take the following features are
available on the diagram page I was so free in a moment but first of all the diagram is
now completed automated but complete Liotta mated every study results can now be using
the old rhythm-based on the GSA diagram. I was are you in a moment is interactive -- you
can zoom in and out talk and highlight certain places of interest that we have consolidated
high-level categories -- this means your colors and abilities to sort of discern the distribution
of the various trait categories among the different symptoms or similarities among the
groups of you are -- if you're so inclined but
>> Many of you are familiar with the PowerPoint progression the chosen number people -- watching
across the various quarters -- we now have that I web and the dynamic time series is
late can the interactive [ Indiscernible ] is the filtering trait.
>> Let me show you the new diagram in the website where it's posted we will put a stop
to this on the [ Indiscernible ].gov webpage -- do they want to see this is a work in progress
the reason I'm showing you the screenshots to be updated with your feedback with other
things on our list. >> So I would just think you that this is,
are here is going to allow you to zoom in and out of the diagram so if you want to highlight
a particular region and click you can it in and even further -- see could see the resolution
is quite nice but the team put quite a bit of effort into choosing the right colors that
would kind of highlight the differences among the groups but if you have for over a particular
trait you can see that I'll bring the hover over that brings -- toes with a trait is.
>> Should also mention that it will give you the other coded legend about what he type
such that you previously. >> So if you click on one tab to the right,
this is a timeseries I was showing you. On the bottom here -- you see that there are
different kind of dots -- this is just a -- a slider that will reiterate -- I will show
you a snapshot 2009. >> Click one tab over and you will find the
filtered diagram -- so this is a diagram of the diagram on diabetes. We have 10 filtered
diagrams available to correspond to the most popular terms through 2011 and 2012. Is lighter
on the bottom reiterates the different diagrams. >> If you click one tab to the right, that
shows you when you can download PG files which are image files of the diagrams -- the use
and if you are still inclined oncology -- ontology vials for the diagram.
>> I don't have time to go into these but if you click on help -- there is also some
additional documentation including where the data come from for your last catalog homepage.
>> So as I alluded to, this is very much a work in progress. What we hope to work on
in the near future includes making your active links from the dock is the other diagram -- on
the catalog data, as well as other geographic that have additional data. Improving featuring
-- filtering features is high on the list but in order to provide an auto complete,
which is where you can type a few letters the system will fill in with additional traits
-- but start with those letters -- as well as the cinnamon -- synonyms but
>> We also hope to develop a pub med ID and, Doyle --
>> So because this is updated we hope to provide a more frequent updated diagram. So currently
it is quarterly and we will go to monthly and perhaps weekly diagram but also high on
the list is improved browser that ability. So if you are at a -- if you are a box fire
Butcher is user the filtering is more limited at the moment. But you can -- the functionality
should be in place. And of course we would like to hear your suggestions.
>> So I would like to thank our catalog team -- and particularly duration side of things
-- Heidi, Heather, [ Indiscernible ], can claim doesn't database design. Darrell Terry
has a -- have been injured until in providing the quarterly updates and I would like to
thank our Holly the DBI -- that were -- and involvement in the data process -- in providing
some additional [ Indiscernible ] and finally for this particular talk as I mentioned most
of the work of the done by Helen Parkinson, Tony project and Danny [ Indiscernible ] have
done an outstanding job on the ontology diagram -- who have a very fun productive collaboration
so without I'm happy to the questions. >> I think this is really good -- it is valuable
but it is a huge job -- I know making the visuals is a lot of work. But something that
once it is done it is an engine and you just add to it and everybody can use it.
>> That is the idea behind automating it -- it is sort of a old rhythm -- and want to make
it look as familiar as it could be because I think people tend to recognize and the quarterly
diagrams that we have so -- there really is no substitute for judgment and discernment
and visual acuity. But we are kind of getting as close as we can. And then when you say
-- >> And then you said it is funded by grants
-- who is that grant to -- >> To just to backtrack -- the grant is to
EBI. The supplemented to do some of the work. >> So that is a [ Indiscernible ] award so
that continuing -- >> Is currently supplemented as a supplement
-- funded as a supplement but >> I think this is really nice. In the visualization
is great but I just -- I notice as long as we have got this interaction -- it would be
kind of nice to actually get exact locusts -- locations of these -- when you roll over
you get the -- what it is associated to -- we don't get its location.
>> It's set -- [ Indiscernible - multiple speakers ] Because they have it -- why not
-- why not you know -- rollover -- [ Indiscernible ]
>> So one of the things would like -- [ Indiscernible - multiple speakers ] At least have it as
an option. >> One of the things we're hoping to do is
have that cover over directly to the catalog -- [ Indiscernible - multiple speakers ]
>> But we can include that in the hover over as well. If you're only seeing one label at
once -- and so adding it is not -- [ Indiscernible - multiple speakers ]
>> And it will be visually -- yes -- and we want to does kinda reinforce it -- the diagram
-- the underlying -- we want to point people to the actual data.
>> So now that you have got it driven by ontology -- you have the option of actually driving
it by alternative ontology -- for simple can you go in and use -- go function or no process
-- to drive that. I think I would be extremely powerful
>> That's a good question -- and actually the use that though -- so no ontology can
be incorporated easily. Because I think we have a lot of emphasis on diseases. I think
what other people mention [ Indiscernible ] we can explore that as well but we can go
with that incorporated your. Snack is that of the really great you can actually use a
code term -- you know -- and you're a go term. >> So one thing that would be made available
is I know that when they have a chance to incorporate this they will exceed [ Indiscernible
] will it believe include all of the go terms -- so for example the catalog for coronary
heart disease can do something else -- that may not be the best example -- it will also
bring up the synonyms. >> Yes -- I guess -- I don't -- I don't know
-- how granular it is -- you might end up with a lot of applications there -- if it
is not regular enough. >> But I will go the right direction.
>> We take your point. So we should go specifically a way of terms to go search.
>> Like the anthology Wirral -- it would be really cool if they could open the ontology
and apply. >> That would be extremely powerful but
>> Thank you for that. >> Mike.
>> This is a really useful tool and I've got were going this way. The animation is great.
Is anything happening on animation in terms of the data-gathering or is it still very
much a manual process? >> We are exploring ways to make it better.
I think we probably will be working on that in the near future. Is definitely one of those
areas where it is obvious there is a need, but we expertise.
>> If we chose the manual process becomes overwhelming -- I'm not sure if it is -- but
if it does become -- they very low bar or high bar to pay a higher looking at it -- if
it came to gosh we really don't know what we can do justice to this -- it would not
be a terrible sin. >> Yes I think that is a good point. In fact
I think there's always it have to be some aspect of filtration -- I think the data mining
can provide [ Indiscernible ] but does having done this -- we have at least for the foreseeable
future want to make sure that we should meet the criteria and you can automate and they
sure the Association is in line with the criteria for the judgment call but
>> And that is the case which I think is perhaps absolutely right but I think it is more for
to make sure we get all the significant results -- white significant results in the paper
rather than getting everything [ Indiscernible ] because honestly in this context -- it is
to the lead up an interesting. And at -6 versus seven -- those are imprintable orders of magnitude.
They will be quite because the papers won't even talk about the 10 to the minus this -- but
it could be good point. >> You mentioned the most common search term
-- do you also have some sense of who the biggest users of the G. what catalog are.
>> Like to pull that up -- we have the user logs that show the idea for this. So we could
probably look at that. >> I don't know off the top of my head.
>> I look at it frequently, but I would be curious how much of the users are researchers
versus positions versus interesting public [ Indiscernible ] with something that they're
struggling with but because I think that also that influences what type of features might
be the most useful to have to build in the future. Like if 90% are users of researchers
-- then the kinds of things that you want to easily link to our right to the position
or given the encodes elements -- and that sort of thing. Where a lot of the users are
looking at it for different reasons, and if this is on the graphics, etc. -- you know.
But I think you have to know that. >> Good point.
>> Disaster really quickly -- in a conversation I had with somebody at a CBI a little while
ago they told me they could not capture the IP address until -- until the who it was that
is looking at material they put up on their -- is that true or not --
>> That is honestly not my area. The I could've misspoken. I will check on that.
>> The issues of whether the government was allowed to capture the kind of information
but >> Unfortunately I don't know the answer to
that. But I will look into that. >> [ Indiscernible audience question or comment
] [ Laughter ] >> I think they have a judge standing behind
them -- [ Laughter ] [ Indiscernible - multiple speakers ]
>> We will look into that for you. >> I know I have been given summary information
about who has various NHI websites -- I don't know the level of detail -- we can try to
find out. I don't know what they were saying they could not find. See that they said they
should tell me it was [ Indiscernible ] -- nothing more specific than that -- [ Indiscernible
- multiple speakers ] Maybe I misunderstood -- probably right -- I can tell you a country
it's from and to things like that. But I don't know the level of resolution we could find
out. The that that may be -- some academic --
>> You know -- culinary indicator -- [ Indiscernible ]
>> How does this look into the say you see a CMD and you're looking at the browser of
that gene -- how could you then can access to all the steps that have the Association
data back -- [ Indiscernible ] because that's the kind of information you want to get when
explaining a gene -- with other associations are there.
>> So they could do specific example you gave -- we don't currently do that in the catalog
-- we start with steps a sickly and RSM or switch you can browse directly or download
directly from the catalog -- the example you gave might be a better fit for another resource
[ Indiscernible ] type integrator -- some of us collaborate with [ Indiscernible ] and
that's a more comprehensive -- comprehensive data from the US catalog -- to other resources
I see in these genes and hopefully in the near future and other data as well but
>> Thank you. >> Yes we can certainly -- we can certainly
at that -- and I would be happy to update on it.
>> This is really great -- you showed us these directive diagrams like you handed a toy to
get a Christmas and all of us are sitting around here playing with us -- playing with
it. And I wanted to -- what I was hearing from people -- all kinds of suggestions and
I would like to generate it -- now that you have got these interactive displays -- you
effectively have a really good deal browser for this kind of research and if there was
some way to set up a query page to query on the field and the catalog of the display them,
we would have control over with the value that you want. What terms we want.
>> And I think -- I mean it be that many more steps. I think it is interactive display -- and
now this is that is useful again so great work and keep it up but
>> It wasn't might work -- congratulations. Thank you very much.
>> -- Any other questions ask -- ask --? Thank you very much
>> So the next presentation is going to be by Mark Dyer and what I asked Mark to do -- if
you listen to my directors report -- when I got to the common fund I talked about sort
of the phasing out of some common fund project like at the libraries we have been involved
in. And I talked about diverse upcoming projects on diagnosed disease per grams and about a
project in between is to in terms of where they are in the lifecycle.
>> These assay and relates to discussions with had are comparable -- before about about
other programs are heavily involved in having it become initiatives -- that has lots of
advantages -- I will state it equivalently -- without knowing the numbers offhand -- we
are by far more involved in common fund -- -- I forgot the common fund projects -- is it eight
or nine or 10 -- nine -- and then annexed Institute has like to oxo it is -- not even
stand out -- and many of them are obvious -- but the components of the program so maybe
it was important to give an update at a council meeting if there's time for this so that you
can service the big picture about all the different result abilities we have for the
common fund. And so that's what Mark is going to give you a bit of a scorecard about where
things are I also think it gives you a complete you of our involvement that is leadership
response ability for different common fund initiatives. The Mac so just to make sure
everybody knows what the NIH, and fund is -- before I start there -- the 2000 the 2006
and H. Reform Act established in the age common fund is a -- NIH common fund as a money under
control and the NIH director with a specific purpose of supporting forward-looking projects
that had brought application across many of the missions -- many if not all of the NHI
institutes but which no one Institute itself can take charge of it leave.
>> And there have been several different processes that we have gone through since 2006 to identify
such projects and to get them up and running. But at the moment, there are now 27 of these
projects that have been initiated. >> In the range from very basic -- let's see
-- something like at which gnome as or no medicine -- through very applied reported
measurement information center and so forth. In each of these projects is managed on the
-- on behalf of the NIH by the ICs. And for each project that will -- at least to ICs
are Institute centers are designated as the only. Or maybe three or even four on occasion.
>> And then any Institute that has interest in being involved in the development of the
ideas and the management of program is welcome to add one or more members to the working
group. So each of these projects has a lead or co-lead Institute and that a working group
consisting of staff from all the Institute's that have interests. So for what Eric is saying
is for the project -- these are the projects that energy just -- NAT arrived as a coleader
of. So out of 27 there are nine. I was right. Nine. So a third of the common fund projects
have an HG are I -- NHGRI is a coleader . And in many cases this is our Institute really
takes the major role among -- even among the co-leads.
>> And those are the programs in the common fund programs that in addition with staff
that had been participating in the working groups.
>> And they were talking about someone over half the common fund projects at that NHGRI
are involved with in one way or another. >> And the actually are a couple others at
still your communication which is a relatively new one were would probably should have somebody,
but don't. And are are one or two that are being developed now. Where staff is actively
participating. >> That's basically the point that I wanted
to make by this talk. They put in -- I think I finished it over the weekend -- I think
it's going into the Council -- if it hasn't it will be -- just a table of a little bit
more information about both the programs for which NHGRI as a co-lead and here is the dollar
figures that I used earlier in coming up with $200 million in total amount of funding from
the common fund. For FY 12 in each of those programs.
>> Common fund programs all have a finite lifetime. They are originally we were up to
10 years. And generally made as either two or three your pilots before they really got
going. Or the five-year phase -- the first phase and then a very hard review to determine
whether they were still relevant and still important for another five years. But it was
the tenure max. The trend more recently -- the last couple years -- to me Carter for common
fund programs to actually go for 10 years. Has they are trying to generate -- they sort
of reached the maximum amount of funds available for common fund programs. And now the only
way that you get money for new common fund programs is either if the NIH -- the total
NIH budget increases, then the common fund can increase in proportion or else by turning
over existing programs into new programs. >> So for H3 Afrika four for instance -- which
terms of all the development work we did in planning with everything we heard said you
really have to have a long-term commitment to this effort. To have a chance for them
to be sustainable. But we were we cannot even announce it as a potential tenure program
-- we had to announce it is a five-year project and if it goes well, then we come to review
and if we did will review, there's a good chance that it will be continued for a second
five years. >> But were not even allowed to mention tenures.
>> I was just curious -- you know you talk about sort of the short pilots and then moving
into the funding work. I assume the pilot years count towards the tenures -- right.
>> Yes. >> So detects is an example of one of the
projects that started as a pilot. It was initially started as a two-year pilot with a purpose
with the goal of simply demonstrating that enough donors can be obtained and that RNA
sufficient quality can be obtained by multiple issues was more to him. It actually -- it
took almost 2 years to collect the data so the pilot was extended for a [ Indiscernible
] year analysis -- but now the the analysis is done and is shown to be very feasible and
informative -- it has been renewed for another five years.
>> So as I said -- an HG are I -- is a co-lead for these programs -- therefore -- and then
five and then you have this information available to you. And then there are several other programs
where we participate in the working group that are also shown on the table so I think
I will stop there rather than going into the individual programs -- Eric give you some
highlights this morning. The triggers in the middle of them -- for five of them will continue
to bring to update you writerly with these programs, these projects in the director's
report but we want to give an overall picture of how deeply involved NHGRI is in this major
effort on this. >> Rick.
>> I think it is great. One of the hallmarks of the Institute that reaches out -- way more
than others. >> How are you taking these on -- to become
to you or do you solicit them -- that's one thing. And the other is -- when you say by
far, you get the percentage [ Indiscernible ] you see the list -- huge number -- you don't
have the staff -- sorry -- your staff has a significant portion of time on this -- because
that's what we're talking about this morning but
>> [ Indiscernible - multiple speakers ] >> Would you put back up -- see if you can
put back up -- is actually a column in their that listed the staff commitment we have for
each of those projects but >> To be fair we get funds from the common
funds -- so our -- with a we do not have anything to do the comment fun, we can have a smaller
staff so these are not -- while -- it is the people's backs because they want to do in
many cases -- the truth of the matter is we have a larger staff to -- the common fund
-- and in those -- and so forth -- so we just -- it indicates how many individuals of the
common fund is providing resources for in terms of salary and so forth.
>> [ Indiscernible audience question or comment ]
>> Correct. >> So we put it in -- we develop a proposal
for the common fund to develop it budget that we include so called RMS -- staff travel and
so forth and so on but however I will say that this -- that doesn't really capture all
of the an HG costs -- things like the actual graph management [ Indiscernible ] to help
pay for -- we don't recover costs -- the budget office administrative costs we don't completely
[ Indiscernible ]. >> Would you benefit -- and this relates to
the first question like how do these come through -- everyone's a different story that
to be honest with you, the fact that some of these were ideas that Frances had and he
ate debated in this Institute when he was a director but and then either -- he became
a cotton fund or the common director and -- these are not all fully dependent phenomenon but
some of it is we have ideas -- and everything we hear they go through different process
of nomination part of new common fund initiatives -- and we are often there in the middle of
putting things forward but I will tell him to be honest -- the latest addition -- the
undiagnosed program -- I had no idea it was going to end up in the common fund but it
was a corporate issue that had to be solved at the and H. level but we work very hard
with Frances to figure out the best long-term -- being done through a very short of sort
term funding arrangement that had to be fixed. In the next phase but it was clearly a successful
program so that with the Institute getting together and directors getting together debating
different options. And at the end of the day they said this just feels like common fund
-- and we developed a larger network and so forth. And so that was the Institute directors
basically endorsing the proposing the idea that it should go into the common fund and
Frances agree to it. >> So that's an example that we were looking
for is to manage the units louche and but I will tell you similarly you told -- heard
about this morning read reports -- three report of the working groups from the advisory committee
of the director -- was data informatics and the data being one of three -- all three of
those are being looked at as possible new common fund feedback projects worked issues
and some of the others are third working group as well.
>> So they come from different means. And an integrated and they also get decided the
same thing happens even with pilot projects that some of them they fund is pilots and
then they decide whether to something as well but
>> The last three or four years -- [ Indiscernible - low volume ] Has made an effort to reach
out to the community for ideas as well. And have [ Indiscernible ] or one or two meetings
-- either by -- mostly by invitation. They started off inviting a lot of senior people
to one meeting in the next year they wanted to invite junior people. At the start of their
career just to talk about areas in which common funds projects would be appropriate.
>> And I would say one last thing -- the other reason of course why we have responsible for
so many -- is purely cultural. And so much of what the common fund does -- it sort of
top-down management we focused community oriented objects that -- but guess what -- that is
our culture that the worker that. And they turn to us and many of them are not disease
specific and very enabling. And that is just what were good at. Mac but after think it's
a sign of the totally awesome power of genetic. And [ Indiscernible ].
>> Yes but >> Do you have a draft of the budget of the
common fund over time but I mean I'm just curious as to whether or not the enabling
structural kind of percentage of money that's going to that has increased over time are
not. >> I don't have it with me -- the answer is
yes. The legislation that established the fund started out at 250 million an increase
in $500 million over the years. And now staple level at five [ Indiscernible ] like all the
rest of us they are sort of flat. >> Other -- questions or comments but
>> Okay but >> Great. Thank you Mark but
>> So I think we are scheduled for a break now. Isn't a good time for a break but so
here's what we're going to do -- we're going to take a break and then we come back we are
going to do the one consequence we have not discussed it and if the time is just right
that we will be done with that at four o'clock which is when we will move to the last topic
related to the into research program. >> So I'm thinking we should reconvene at
10 after -- quarter after. >> Quarter after a so I guess the place of
stairs is open now for another 55 minutes -- but we will reconvene then at 3:15.
>> Thank you very much.