>> Welcome to the overview of the caNanoLab Data Portal,
caNanoLab was built through a collaboration with the NCI Center for Biomedical Informatics and
Information Technology and the Office of Cancer Nanotechnology Research.
caNanoLab 2.0 was just released recently and I'm going to give an overview
and demonstration throughout this presentation of the new release of caNanoLab.
First some background information, caNanoLab Data Portal,
our initial goal was to build a portal to provide a nanotechnology resource
that really enables and fosters data sharing in the research community
with hopes of expediting and validating the use of nanomaterials in biomedicine.
And working with the community we went through a couple of scientific questions
and use cases that really, when you look at them, are informed through data sharing.
These are just three that I've selected for this presentation,
the first, the scientists wanted to know the effects of nanomaterials size and shape on biodistribution.
This was one that was discussed during one of the informatics sessions
at the NCI Nano Alliance and I think it really illustrates
that you do need a lot of different information on different types of particles,
the different size and shape of those particles
and how they effectively biodistribute throughout the organism.
The next question is the existing drug used to target cancer causes significant side effects,
can nanomaterial-assisted targeted delivery increase efficacy
and reduce side effects? This is one of the questions
that we're typically asked during the nano working group meetings that we have
and as you can see it really does require looking at the composition
of the particle and other components of the particle to see
if there will actually be a decrease in side effects
as compared to traditional approaches.
And the last, we worked with different modeling and simulation vendors
who are looking at the effects of nanomaterial properties on toxicity
and in order to complete their modeling and simulation they really need access
to high quality and complete data sets.
So as you can see we really need a nanotechnology platform
and resource that provides access to high quality and complete data sets,
that allows us to answer some of these and other scientific questions.
caNanoLab, as I said, we originally designed it to facilitate data sharing
in the community, it does provide support for the annotation of nanomaterials
with the composition information and characterizations. Some of the characterizations
we capture are physical chemicals, some are in vitro and some are in vivo.
We originally started developing caNanoLab from based on use cases from the NCI's Nanotechnology Cancer Laboratory,
a characterization laboratory, as well as the NCI Alliance for Nanotechnology in Cancer.
I'm going to go right to the home page of caNanoLab and just kind of walk you through that.
This is the caNanoLab home page when you go
to the home page there's some related links and some external links as well,
there's information on a user's guide as well as a glossary for some of the terms that we use in caNanoLab.
The center here allows you some facilities to browse,
so if you want to do some search for protocols,
for samples or publications you can click on these links and when you click
on those links you'll get a search form
that you can further do some searches of that information.
We also have the results here, some statistics of the publically available data that we have.
Currently we have over 1,000 samples that are publically available for you
to download and view as well as over 1,800 publications.
On the right here we have some user actions,
obviously without logging in you can just browse publically available data.
You can log in if you want to submit data or browse data
that you previously submitted in a controlled fashion,
you would log into the system,
you can also register for a log in account or reset your password.
We also have some information on some how to's and some link
if you want some information on how to submit data in caNanoLab,
how you can incorporate caNanoLab into a data sharing plan.
You can click on these links and go to the caNanoLab FAQ.
We also provide caNanoLab in the open source community
so you can download the software if you would like
and use that in your organization.
So I'm going to jump back to the presentation,
caNanoLab was built on some high-level concepts,
we started with looking at nanomaterial sample
and we looked what were the other concepts that we needed to capture,
we need to capture the composition of a particle
and that typically includes the base nano particle
which is the nanomaterial entity
and a particle can have multiple nanomaterial entities, if it's
like a complex particle like a liposome embedded in a quantum dot.
Then there's some functionalizing entities associated with the particle,
these are entities that are associated with particles
that give it a specific function such as therapeutic, targeting, diagnostic,
imaging. And a particle can have multiple functions,
so you would have small molecules, you could have diagnostic, imaging,
contrast agents associated with the particle.
Then chemical associations are the way these components
within the sample are linked, you know, are they attached,
are they encapsulated or are they entrapped?
I'll be showing some examples as we go through that.
The nanomaterial sample also has several characterizations that are performed
on the sample, the characterizations typically use a protocol,
we capture protocols from physical, chemical, in vitro, in vivo,
you can upload and whatever protocols you want associated with the characterization.
There's also we capture information on physical, chemical characterizations,
in vitro characterizations, and in vivo and typically over here are some
of the concepts, high level concepts we capture for the different types
of characterizations and we...I'll be going through those in a little bit.
And lastly you have publications or even reports associated with the sample
and we capture that relationship as well.
This is the workflow of caNanoLab when you log into the system
if you are submitting data you'll see this work flow diagram
that you can then click on to get to the areas you want.
For submission, a user typically logs in, they submit protocols,
they submit samples and submit publication.
Of course when they submit samples they start
with submitting general information about the sample,
information about the composition and the characterizations
and we will be walking through this.
Also there's search facilities, they can search for protocols, search for samples and search for publications.
We're going to start with the protocols,
caNanoLab does support both the submission and retrieval
of nanotechnology protocols, many different types of protocols we support.
We do provide access to standardized protocols from the NCL
that they have worked on, some of them with NIST and protocols can be associated
with characterization assays and when you go to look
at your characterization you can choose what protocol you want to submit.
So I'm going to jump to the application, I'm going to go ahead and I'm going
to select to search protocols and we'll just go ahead
and search for physical, chemical assay protocols.
And when you search that you'll get a list back of the different protocols,
some are videos, some are actually documents,
we're going to go down to select the NIST NCL joint assay protocol, PCC 13,
when you select view it you'll then be able to view the protocol,
the actual PDF file that describes the protocol.
So that's the protocol search capabilities. If we wanted to go in
and actually log into the system I'm going to show you how to submit protocols. [ brief pause ]
You'll be presented as I said with this screen you can kind
of see the work flow diagram that we just reviewed,
I'm going to go directly to protocol and I'm going to select
to submit a new protocol, I'm going to select the pull down list
for protocol type, we'll do a physical chemical assay, you can select other
and if you select other you can type in your different protocol types.
We're just going to say test demo 1 for the protocol name,
when you go into caNanoLab anything that has an asterisk is a required field,
everything else is not required.
You can have an abbreviation for the protocol, the protocol can have a version
and you simply can either upload a file or enter a URL for the file,
we'll just upload just a draft demo file.
You can give the file a title and a description.
You can also change access to the protocol, throughout caNanoLab you can select
who you would like to access the protocol.
You can grant access to a collaboration group, a user or the public.
If you're a general user and want to grant access
to the public, we do have an approval process where it then goes to our curator
who then reviews it prior to making public.
I'm going to go ahead and submit this protocol,
and so the protocol was successfully saved with the test demo so if we go
into search our protocol name, go into search,
okay test we will then be able to retrieve the protocol that we just created today.
If we go back to the presentation, caNanoLab samples you can submit
and retrieve information on the composition of the particle
and as I said earlier, the composition includes the nanomaterial entities,
the functionalizing entities and also the chemical association.
The nanomaterial entities can have composing elements such as a core,
a coat and I'll show you this example in just a minute.
We do maintain different metadata to describe the composition of each particle type so if we go,
here's just an example of particle specific composition metadata that we have,
the particle type for biopolymer we capture the name and the type and the sequence.
For carbon nanotube we look at the wall type, the chirality, the length, dendrimer, branch and generation.
So these are just some of the different metadata you can also add other metadata
when you go ahead and choose to submit a specific particle.
I'm going to go right to the caNanoLab application right now.
For now I'm going to log out so you kind of see a user's, a general user's view,
we're going to search our sample and we're going to search a sample for NCL 23.
NCL 23 is a dendrimer and it has an imaging function associated with it,
we also have the concept of a data availability matrix, which gives you kind
of an understanding of how much data is available for this particular particle.
We take the caNanoLab concepts that we have here and the MINchar concepts
and you'll see a check box next
to whether this particular particle has the information
from these two standards that we're capturing.
When we give it a score, a percentage is calculated based on that.
We're going to go and view NCL 23, here you can see the general information
about the particles, NCL 23 we have some key words associated with, Magnevist,
MRI, we have the organization information.
If we go ahead to the particle caNanoLab the composition we looked at caNanoLab it is a dendrimer,
a generation 4.5 COONa terminated PAMAM dendrimer Magnevist complex
and it has 1 to 4 branches in the generation of 4.5.
We also have a schematic loaded with this dendrimer so you can take a look
at the dendrimer as well as the surface groups associated with the dendrimer.
The functionalizing entity associated with Magnevist and it goes ahead
and gives an imaging function, you can see the chemical structure of Magnevist
and then lastly you can see the association and there is an association
between the core which is diamino butane of a dendrimer
and the functionalizing entity which is a small molecule called Magnevist.
You can also just associate other images as well.
We're are going to jump into characterizations of this particle and in the characterizations
of a particle we have several physical chemical characterizations as well as in vitro characterization.
What you can see is, here's an example
of molecular weight you can see the technique used or and the instruments are also what we support,
there's some characterization results which what we call a data matrix
which allows you to view data and conditions associated with that.
You can take a look at the files that are associated with this characterization as well as the description.
You can kind of see we're capturing several different types
of characterizations associated with this particle.
You can get a view of just the physical chemical characterization,
you can get a view of the in vitro characterizations taking a look
at the different files and also the conditions and data associated with that.
We also have some buttons up here for easy printing,
for exporting so you can actually go ahead and export to Microsoft Excel
so you can get a nice view of the information in a Microsoft Excel
format, where we capture the different characterizations in each of the different tabs in Microsoft Excel.
Okay we're going to go back to the presentation,
so we talked about characterizations and we went through the different types of characterizations, before I get
into the different characterization metadata I kind of just want
to give just a brief overview of submitting a particle in caNanoLab.
So we're going to go ahead and log in and we're going to
select samples and we're going to select to submit a sample, there is a feature in caNanoLab
to copy an existing sample so if you have a characterization that you're doing
and you have several samples that are very similar that are just being altered
in a couple of different components, you can copy the sample then just go
and edit that sample, it just makes it a little convenient.
So we're going to go ahead and just create a demo, a dendrimer sample,
a point of contact, you can kind of see we'll just go ahead and pick a point
of contact, you can also add a point of contact by specifying other,
we'll just select the Nanotechnology Characterization Laboratory.
The role is investigator you can put some address information in there,
we're just going to go ahead and save that.
[ Silence ]
So while the nanoparticle, the general information is being saved I do want to go through a little bit of this.
The different characterization assay metadata we have defined some metadata
for each of the different types and we have been in the process
of reviewing some of these with the community.
We're going to focus on adding a physical chemical characterization today
so you can see we capture molecular weight, physical state, relaxivity, shape,
size, solubility, surface and zeta potential.
You know like I said throughout the system you can also add others as well.
So the point of contact information has been saved,
you can change the access as well to the nanoparticle, I'm going to go ahead
and then choose to add composition information.
We're going to start by adding a nanomaterial entity for the particle
and this is where you specify the different types of particles
and the metadata changes based on the particle.
We're just going to choose dendrimer and this section here has the specific properties,
we're just going to add a branch and a generation.
You then add composing elements and you can add multiple composing elements,
we're going to give this dendrimer a core, we're going to call it diamino butane.
You can choose to link it to PubChem
and you can choose the chemical ID once you save it then cananolab will then associate
a link to PubChem for this particular composing element, you can give an amount,
a molecular format if you'd like using SMARTS, SMILES, and Hill
and then you can also choose to give this particular composing element.
If the composing element itself has a function then you can give
that composing element an actual function.
We scroll down so we added our composing element with the diamino butane,
you can also choose to add a file, you pretty much just upload a file,
we'll just go ahead and upload our cananolab demo file or you can choose a URL.
Here you specify the type of file, you can give it a title,
you can associate keywords with the files and here's also
at the bottom there's an option to then copy this composition to other samples
within the same primary organization.
So if I wanted to...if I had a complex particle
where I had several different components I could go ahead and choose to copy
that and for convenience I would just go back and edit it.
so back to adding the composition information, once the composition information
is added we added a nanomaterial entity, we can go in and sort of use the same approach,
then add a functionalizing entity.
The functionalizing entity is you know like I said, it's a Magnevist particle,
you could give it the different functionalizing entity type,
could be small molecule and other types, a chemical name,
pretty much the same information you would typically see for some
of the nanomaterial entity, except you are going to give it an inherent function.
These are just some of the inherent functions, then really each of the screens while you add a file.
We're just going to go in to go ahead to characterization and I'm just going
to demonstrate adding the characterization. So here's the different types of characterizations
you can certainly add other if you have other characterizations.
I'm going to go ahead and select to add characterization
and the characterization type, characterization name changes based on the type you select.
So obviously if you have in vitro you'll see a list of in vivo,
I'm just going to select size, I'll select just size again for the assay type.
You can then select the protocol version, I'm going to select we'll just do PCC,
PCC 1, and it gives you a link to the protocol.
The characterization source will say the NCL,
you can add the date in which it was characterized.
You can add a basic description of the design and methods,
you can also add the technique and instrument information
so we'll just say dynamic light scattering, you can put DLS.
If you wanted the specific instrument you can also add some of that information, we'll go ahead and save that.
You can add the analysis and conclusion which really is a description of sort
of the overall findings a summary of that.
But you can also add individual findings.
You can upload files associated with the findings,
you can also upload data additions,
I'm going to just to illustrate this create a data matrix that has two columns
and two rows, you then go into the column,
the column type will make this a condition.
The condition we'll call it...we'll say temperature will be our condition,
you can add properties to the condition, you can add a different value type,
we'll just say for this it's going to just going to be an observed, the unit is going to be Celsius.
You can add a constant value, which if you're doing an experiment
that has the same condition, like you're always doing 25 degrees Celsius,
then you add the constant value and it automatically populates.
So our first column is temperature,
our second column is going to be the actual data and what we'll have is
for size we're just going to go ahead and select size at this point
and then our unit will select nanomaterials and so we have our columns
and you just type in the data, we'll just say this is 10.8, we'll say this is 47
and this is 12.2 and we'll go ahead...you can certainly upload a file associated with this as well.
We'll just go ahead and save the findings.
You can add many different columns and many different data,
you can upload all different types of files
and you know caNanoLab will then create the data matrix for that and will also add the file.
You can also choose like the other ones to copy the finding data conditions
and you know if you have several particles where you're doing the same type
of characterization and you're just you know the protocol's calling
for the same temperatures and you're just alternating the value
that makes it a little bit easier when going in and just having to edit.
You can see we added our physical chemical characterization,
you would do the same process for in vitro and the other characterization,
I'm going to then jump back to the presentation.
You can see with in vitro we're capturing characterizations from blood contact,
cytotoxicity, enzyme induction, immune cell function, metabolic stability,
oxidative stress, sterility, targeting and transfection.
In working on identifying the associated metadata
for these characterizations we did start with the characterization assay cascade
from the Nanotechnology Characterization Laboratory and then expanded that based
on our curation of publications and working with the NCI Nano alliance.
In terms of the other types of characterization in vivo we did host a
in vivo characterization working group with several members of the community
as well as other government organizations and we came up with a list of concepts
to capture for the in vivo characterization
such as the pharmacokinetics concepts, toxicology and imaging.
This is in an area where we really do want to expand on as well.
Lastly through some of our publications that are ex vivo types
of characterizations we are capturing some information on histology,
imaging and these are just some of the recommended metadata that we have seen
so for, there is certainly are other examples.
I'm going to go into publications in just a minute,
obviously we support the submission or retrieval of publications and other types of reports.
We do provide access to over 1,000 abstracts that were published
from the Alliance for Nanotechnology in Cancer.
We also have abstracts from the broader nanotechnology community including the
international community.
We do have an auto-completion feature that was implemented for PubMed articles
that leverages the PubMed HTTP API so when you type
in the PubMed ID it then goes ahead and retrieves the PubMed information
from the XML and that just makes it a little bit easier in terms of data entry.
We recently in 2.0 added an interface between a publication vendor
and a caNanoLab and we developed you know leveraging the document object,
the DOI, you can then retrieve information on the sample based on the DOI
and I'll be showing that in a little bit.
So I'm going to go ahead and go to the publications area within caNanoLab
as you can see you can select publications,
we can do a search for existing publications,
you can search by publication type, PubMed, digital object,
you can search by exact title or contains by authors with each author listed
on the line, key words also by sample and the different types of entity.
I'm just going to type dendrimer in this particular search and we'll go ahead
and do search for publications and this will return a list
of publications obviously that have dendrimer in the title.
So as you can see here's a list
of the publications you can view some more detailed information
of the description and also go directly to PubMed using that publication.
So I'm going to then go ahead and go back to publications and I'm going
to submit a new publication, I'm going to go ahead
and submit a peer review article and we'll say it's published,
you can look up the PubMed identifier,
I'm just going to type in arbitrary PubMed identifier for illustration purposes.
As you can see once we enter the identifier
and I selected another column it automatically went out to PubMed and populated all these fields.
You can certainly upload files and publications associated with that if you'd like.
But that really is how you would submit a publication,
you can also enter the digital object identifier.
We're going to go back to the presentation, click, caNanoLab released,
we just released caNanoLab 2.0 it is now available.
On caNanoLab 2.0 with the primary features we'll use the usability enhancements
based on feedback, we did have a caNanoLab survey and got some feedback,
we did change look in field, we added a my work space feature so that
when you go ahead and submit samples,
protocols and publications you can select my work space as you can see here
and you can view all the samples and protocols and publications that you
submitted just for easy access to edit if you want to go back and edit those.
We are working on...we have developed the DOI based interface
that we are working with the publication vendor on,
this kind of just shows the example when you enter a DOI for a search.
You can now get the samples and the characterizations associated with the DOI.
So from the publication vendor's standpoint they'll have the publication nanotechnology
and if that publication has data in caNanoLab you'll see a caNanoLab icon
on the right and you'll be able to click,
a user will be able to click the caNanoLab icon from the publication
and it will launch a caNanoLab with the information on the samples
and the researcher can get to...the user can get to more detailed information
about the sample and the data associated with that publication.
We are working on caNanoLab 2.1 which will be in production later in 2015
and it will include continued usability enhancements. We also want
to do some performance enhancements and some prioritized features based
on feedback from the community.
This is the my work space feature, you get to it from this link,
as you can see here's the sample we added that's attached throughout this
demonstration, you can toggle whether you want to see just samples, protocols and publications.
Here's some protocols that were submitted as well as some publications
and I can just go and edit if I'd like to go in
and edit those directly for convenience.
In terms of the DOI based search this is where we added the search for sample
by publication, I'm just going to go in select copy my DOI and I'll go ahead
and do search based on the DOI and so what's you're seeing is a couple
of things, you have the DOI ID which is a link to the publication,
you have the link to the sample information, you can see the abstract associated
with the publication, you have the links of the characterization.
You also have that preserved in the URL
but the publication vendor actually uses the URL to make that connection.
So that's the DOI based search.
So that's the overview of caNanoLab I hope you enjoyed today's demonstration,
we do have some resources, obviously the production portal that I just showed you here is the URL,
we have a caNanoLab wiki which provides information on caNanoLab you know some
of the demonstration links as well as usage information and users guides.
We do have a usability group that we formed that's on the NCIP Hub
and let me just bring that up really quick.
This is a form, we created a group that allows users to go ahead
and add what we call new feature requests and items to the wish list,
so we get feedback on areas that we can certainly improve on.
So I just encourage...we encourage the use of that because we do highly value the feedback.
Lastly I just want to acknowledge the team,
we have our caNanoLab sponsors from the NCI, Juli Klemm, Mervi Heiskanen,
JJ Pan and Stephanie Morris.
We also have our development team which is listed here
from Leidos Biomedical Research and the NCI group
and then we have a curator Michal Lijowski
who has been actively curating data for us in caNanoLab.
So thank you very much for your attention,
I hope you enjoyed this demonstration.