src/scenes/Help/Faq.js
import React, { Component } from "react";
import { Link } from "react-router-dom";
import { HashLink } from "react-router-hash-link";
import { scrollTo } from "~/utils/utils";
import "./Help.scss";
class Faq extends Component {
constructor(props) {
super(props);
this.downloadUrl = process.env.REACT_APP_DOWNLOAD_URL;
}
render() {
return (
<div className="content-block section" id="faq">
<h2 className="content-block-heading">Frequently asked questions</h2>
<div className="content-block-content">
<div className="faq">
<div className="faq-q">
How can I search for data about metabolites?
</div>
<div className="faq-a">
<p className="no-bottom-margin">
Metabolites can be searched via their names; synonmys;
descriptions; BioCyc, CAS, Chemspider, ChEBI, KEGG, and PubChem
ids; and InChI and SMILES representations. Below are several
example queries for metabolites.
</p>
<ul className="no-top-margin">
<li>
Name: <Link to="/search/Adenosine/">Adenosine</Link>
</li>
<li>
BioCyc id: <Link to="/search/ADENOSINE/">ADENOSINE</Link>
</li>
<li>
CAS id:{" "}
<Link to={'/search/"58-61-7"/'}>"58-61-7"</Link>
</li>
<li>
ChEBI id: <Link to="/search/16335/">16335</Link>
</li>
<li>
Chemspider id: <Link to="/search/54923/">54923</Link>
</li>
<li>
KEGG id: <Link to="/search/C00212/">C00212</Link>
</li>
<li>
PubChem id: <Link to="/search/60961/">60961</Link>
</li>
<li>
InChI:{" "}
<Link
to={
'/search/"InChI%3D1S%2FC10H13N5O4%2Fc11-8-5-9%2813-2-12-8%2915%283-14-5%2910-7%2818%296%2817%294%281-16%2919-10%2Fh2-4%2C6-7%2C10%2C16-18H%2C1H2%2C%28H2%2C11%2C12%2C13%29%2Ft4-%2C6-%2C7-%2C10-%2Fm1%2Fs1"/'
}
>
"InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1"
</Link>
</li>
<li>
InChI key:{" "}
<Link to={'/search/"OIRDTQYFTABQOQ-KQYNXXCUSA-N"/'}>
"OIRDTQYFTABQOQ-KQYNXXCUSA-N"
</Link>
</li>
<li>
SMILES:{" "}
<Link
to={
'/search/"[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=NC3=C2N=C([H])N=C3N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]"/'
}
>
"[H]OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=NC3=C2N=C([H])N=C3N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]"
</Link>
</li>
</ul>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I search for data about classes of genes (ortholog
groups)?
</div>
<div className="faq-a">
<p className="no-bottom-margin">
Ortholog groups can be searched via their names;{" "}
<a
href="https://www.orthodb.org/"
target="_blank"
rel="noopener noreferrer"
>
OrthoDB
</a>{" "}
ids; and the names, symbols, NCBI and UniProt ids, and EC
numbers of individual genes. Below are several example queries
for genes.
</p>
<ul className="no-top-margin">
<li>
Name:{" "}
<Link to="/search/Glutamate dehydrogenase/">
Glutamate dehydrogenase
</Link>
</li>
<li>
OrthoDB id:{" "}
<Link to="/search/692851at2759/">692851at2759</Link>
</li>
<li>
Gene symbol: <Link to="/search/GLUD1/">GLUD1</Link>
</li>
<li>
NCBI Gene id: <Link to="/search/2746/">2746</Link>
</li>
<li>
UniProt gene id: <Link to="/search/P00367/">P00367</Link>
</li>
<li>
EC number: <Link to="/search/1.4.1.3/">1.4.1.3</Link>
</li>
</ul>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I search for data about classes of reactions (Enzyme
Classification groups)?
</div>
<div className="faq-a">
<p className="no-bottom-margin">
Enzyme Classification groups can be searched via their names, EC
numbers, and reactants and products (names and InChI key
representations). Below are several example queries for
reactions.
</p>
<ul className="no-top-margin">
<li>
Name:{" "}
<Link to="/search/Glucose-6-phosphatase/">
Glucose-6-phosphatase
</Link>
</li>
<li>
EC number: <Link to="/search/3.1.3.9/">3.1.3.9</Link>
</li>
<li>
Reactant/product names:{" "}
<Link to="/search/D-glucose/">D-glucose</Link>
</li>
<li>
Reactant/product InChI keys:{" "}
<Link to={'/search/"NBSCHQHZLSJFNQ-GASJEMHNSA-N"/'}>
"NBSCHQHZLSJFNQ-GASJEMHNSA-N"
</Link>
</li>
</ul>
</div>
</div>
<div className="faq">
<div className="faq-q">
Does <i>Datanator</i> include data about multi-cellular organisms?
</div>
<div className="faq-a">
Yes, <i>Datanator</i> has a significant amount of data about
several multi-cellular organisms. In fact, four of the five
organisms best characterized by <i>Datanator</i> (most
measurements) are multi-cellular. These four organisms are{" "}
<i>Arabidopsis thaliana</i>, <i>Homo sapiens</i>,{" "}
<i>Mus musculus</i>, and <i>Rattus norvegicus</i>. Where possible,{" "}
<i>Datanator</i> tracks the source cell line, cell type, and
tissue of each measurement of a multi-cellular organism.
</div>
</div>
<div className="faq">
<div className="faq-q">
Why are RNAs and proteins grouped by ortholog groups rather than
by gene names or UniProt ids?
</div>
<div className="faq-a">
<p>
To help researchers find relevant data in the face of sparse
measurements, one of the goals of <i>Datanator</i> is to help
users find potentially relevant measurements of similar
molecular biology (e.g., similar metabolites, RNA, proteins,
reactions) in similar organisms (e.g., neighboring taxa) and
environmental conditions (e.g., similar temperature, pH). For
RNA and proteins, this is achieved by displaying measurements of
the RNA/protein of interest, as well as measurements of
orthologous RNAs/proteins.
</p>
<p>
<i>Datanator</i> uses OrthoDB's ortholog groups because
they have wide taxonomic coverage, they have been generated via
an unbiased, systematic approach, they are available in a
machine-readable format, and they are available under an
open-source license.
</p>
<p>
<i>Datanator</i> uses orthology rather than gene names to
identify similar RNAs/proteins because gene names are not
consistent across organisms (similar genes can have different
names, and genes with similar names can have dissimilar
sequences). Similarly, <i>Datanator</i> uses orthology rather
than UniProt ids because each UniProt id only refers to a single
gene in a single organism.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How does the search form use the taxon input?
</div>
<div className="faq-a">
<p>The taxon input is used for two purposes in the data pages:</p>
<ul>
<li>
<b>Sorting:</b> The taxon input is used to sort the
potentially relevant measurements by their taxonomic
similarity to the taxon of interest.
</li>
<li>
<b>Filtering:</b> The taxon input is used to provide users a
slider for filtering the potentially relevant measurements by
their taxonomic similarity to the taxon of interest.
</li>
</ul>
<p>
Note: due to the computational cost of calculating taxonomic
similarity, the taxon input is not used to filter or rank search
results. Going forward, we hope to use the taxon input to
provide more relevant search results.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
The search results don't appear to be limited to the taxon
entered in the search form. Why isn't the taxon input used?
Why does the search form ask for a taxon? Where is the taxon input
used?
</div>
<div className="faq-a">
<p>
The search form asks for a taxon because, as described above,
the data pages uses the taxon input to sort and filter
potentially relevant measurements by their similarity to the
taxon of interest.
</p>
<p>
In designing <i>Datanator</i>, we felt that the simplest and
most intuitive way to help users find data relevant to specific
organisms is to begin by asking users both about (a) the
molecules or reactions they want to find data about and (b) the
taxon (organism) they would like data about. From the start,
this design intentionally encourages users to think about
finding data relevant to specific taxa. In particular, we felt
this design was simpler than providing a form on each data page
which asks users to enter their taxon of interest and uses this
information to sort and filter measurements.
</p>
<p>
Due to the complexity of calculating taxonomic similar,
unfortunately, the search results do not yet filter or rank
search results by their taxonomic similarity. The taxon input is
only used to sort and filter measurements in the data pages.
</p>
<p>
<i>Datanator</i> also aspires to help users find data from
relevant environmental conditions. Ideally, this would be
implemented symetrically by incorporating an input for the
target environmental condition in the search form, and using
this information to filter and rank the search results, and sort
and filter the potentially relevant measurements in the data
pages. We have chosen to implement filtering and sorting of
environmental conditions differently from filtering and sorting
taxa (genotypes) for several related reasons: environments
require multi-dimensional descriptions (e.g., temperature, pH,
gas pressures, media) which makes capturing the target
environment and computing environmental similarity more complex,
there is no commonly accepted way of systematically describing
environments (e.g., no ontology of media), and <i>Datanator</i>{" "}
does not consistently represent the environmental condition of
each measurement because the sources that we have used to
assemble <i>Datanator</i> provide different metadata (i.e. some
sources record temperatures while others do not). We aspire to
improve this going forward. In our opinion, this requires a
community effort to annotate environmental conditions more
consistently which, in turn, requires the development of data
models and ontologies for describing environmental conditions.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
Why does the metabolite concentration data table display data for
biomolecules that were not queried (e.g., ADP is displayed in the
page for ATP)?
</div>
<div className="faq-a">
<p>
To help researchers find relevant data in the face of sparse
measurements, <i>Datanator</i> displays measurements of the
queried metabolite, as well as measurements of structurally
similar metabolites.
</p>
<p>
<i>Datanator</i> uses the{" "}
<a
href={
"http://openbabel.org/docs/dev/Features/Fingerprints.html"
}
target="_blank"
rel="noopener noreferrer"
>
Tanimoto coefficient
</a>{" "}
to evaluate the structural similarity of metabolites. By
default, <i>Datanator</i> displays measurements of metabolites
that have Tanimoto coefficients of 0.65 or higher. The
"Chemical similarity" filter can be used to narrow the
displayed measurements to measurements of highly similar
metabolites (Tanimoto coefficient near 1).
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can <i>Datanator</i> help me find data measured in similar
cell types?
</div>
<div className="faq-a">
<p>
<i>Datanator</i> aims to help users leverage all available
metadata to find data relevant to a specific species, genetic
variant, and cell type. Note, this is limited by the metadata
reported by the original authors and the primary databases that{" "}
<i>Datanator</i> integrates.
</p>
<p>
All of <i>Datanator</i>'s data tables provide information
about the organism in which each measurement was conducted. This
information can be filtered to find data measured in closely
related organisms.
</p>
<p>
In addition, the measurements in the protein abundance table can
be filtered by tissue type, and the measurements in the reaction
rate constants table can be filtered by whether the measurement
was conducted in a wildtype or mutant strain.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can <i>Datanator</i> help me find data measured in similar
experimental conditions?
</div>
<div className="faq-a">
<p>
<i>Datanator</i> aims to help users leverage all available
metadata to find data relevant to a specific experimental
condition. Note, this is limited by the metadata reported by the
original authors and the primary databases that <i>Datanator</i>{" "}
integrates.
</p>
<p>
The measurements in the metabolite concentration table can be
filtered by growth media, growth phase, and growth conditions.
The measurements in the reaction rate constants table can be
filtered by pH and temperature.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
What kinds of models or other analyses does <i>Datanator</i>{" "}
facilitate?
</div>
<div className="faq-a">
<ul className="vertically-spaced">
<li>
<i>Datanator</i> can help investigators find genomic and
biochemical data to identify the <b>initial conditions</b> and{" "}
<b>rate parameters</b> of{" "}
<b>continuous and stochastic dynamical models</b>. In turn,
this can help investigators construct more comprehensive and
more accurate models.
</li>
<li>
<i>Datanator</i> can help investigators improve{" "}
<b>constraint-based models</b> of metabolism by helping
investigators find enzyme abundances and reaction velocities
to <b>bound the fluxes</b> of chemical transformation and
transport reactions.
</li>
<li>
<i>Datanator</i> can help investigators modify{" "}
<b>
models to capture other organisms, tissues, and cell types
</b>{" "}
by helping investigators find data to re-calibrate model
parameters. In turn, this can help investigators compare
organisms, tissues, and cell types.
</li>
<li>
<i>Datanator</i> can also help investigators conduct{" "}
<b>data-driven meta-analyses</b> of molecular biology. For
example, the <i>Datanator</i> database can be used to conduct
multi-dimensional analyses of an individual organism or
conduct comparative analyses of multiple organisms.
</li>
</ul>
</div>
</div>
<div className="faq">
<div className="faq-q">
What modeling tasks does <i>Datanator</i> facilitate?
</div>
<div className="faq-a">
<i>Datanator</i> can help modelers accomplish several tasks:
<ul className="vertically-spaced">
<li>
<i>Datanator</i> can help modelers <b>design</b> the scope and
granularity of a model by helping modelers assess the data
available for calibration and validation.
</li>
<li>
<i>Datanator</i> can help modelers find data to{" "}
<b>calibrate</b> the parameters of a model.
</li>
<li>
<i>Datanator</i> can help modelers find independent data to{" "}
<b>validate</b> the predictions of a model.
</li>
</ul>
</div>
</div>
<div className="faq">
<div className="faq-q">
Can I programmatically access the data in <i>Datanator</i>?
</div>
<div className="faq-a">
<i>Datanator</i>'s REST{" "}
<a
href={"https://api.datanator.info/"}
target="_blank"
rel="noopener noreferrer"
>
API
</a>{" "}
can be used to programmatically access <i>Datanator</i>. Please
see the{" "}
<a
href={"https://api.datanator.info/"}
target="_blank"
rel="noopener noreferrer"
>
documentation
</a>{" "}
for more information.
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I download all of <i>Datanator</i>'s data?
</div>
<div className="faq-a">
<p>
<i>Datanator</i>'s data is available as a MongoDB snapshot
from{" "}
<a
href={this.downloadUrl}
target="_blank"
rel="noopener noreferrer"
>
Zenodo
</a>
. The content of the <i>Datanator</i> database is a compilation
of data curated by the Datanator Team and data aggregated from
third-party databases. The copyrightable content curated by the
Datanator Team is available under the Creative Commons 1.0
Universal Public Domain Dedication (CC0) License. The content
from third-party sources is available under the licenses
summarized on the{" "}
<HashLink scroll={scrollTo} to="/about/#license">
About page
</HashLink>
. The structure of the database is available under the CC0
License.
</p>
<p>
In addition, users can use the
<a
href={"https://github.com/KarrLab/datanator"}
target="_blank"
rel="noopener noreferrer"
>
{" "}
<i>Datanator</i> software
</a>{" "}
to construct their own version of
<i>Datanator</i>'s database. This will download the data
from the primary sources and parse, normalize, and integrate the
data into a single database.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I use the <i>Datanator</i> MongoDB snapshot?
</div>
<div className="faq-a">
<p>First, install and configure MongoDB.</p>
<p className="no-bottom-margin">
Second, restore the snapshot by executing the following
commands:
</p>
<pre>
lvcreate --size 1G --name mdb-new vg0{"\n"}
gzip -d -c mdb-snap01.gz | dd of=/dev/vg0/mdb-new{"\n"}
mount /dev/vg0/mdb-new /srv/mongodb
</pre>
<p>
Please see the{" "}
<a
href={
"https://docs.mongodb.com/manual/tutorial/backup-with-filesystem-snapshots/"
}
target="_blank"
rel="noopener noreferrer"
>
MongoDB documentation
</a>{" "}
for more information about restoring snapshots.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I cite <i>Datanator</i>?
</div>
<div className="faq-a">
<p>Please cite the following article.</p>
<p>
Roth YD, Lian Z, Pochiraju S, Shaikh B & Karr JR. Datanator:
an integrated database of molecular data for quantitatively
modeling cellular behavior. bioRxiv, 2020.08.06.240051 (2020).
DOI:{" "}
<a
href="https://doi.org/10.1101/2020.08.06.240051"
target="_blank"
rel="noopener noreferrer"
>
10.1101/2020.08.06.240051
</a>
.
</p>
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I contribute data to <i>Datanator</i>?
</div>
<div className="faq-a">
Please{" "}
<HashLink scroll={scrollTo} to="#contact">
contact us
</HashLink>{" "}
to discuss how to integrate your data into <i>Datanator</i>. We
are particularly interested in molecular data about metabolites,
DNA, RNA, proteins, complexes, and reactions such as RNA
abundance, protein half-lives, and RNA and protein modification
and localization.
</div>
</div>
<div className="faq">
<div className="faq-q">
How can I contribute to the development of <i>Datanator</i>?
</div>
<div className="faq-a">
We would love to work together to integrate data for biomodeling.
Please{" "}
<HashLink scroll={scrollTo} to="#contact">
contact us
</HashLink>{" "}
to discuss how to get involved.
</div>
</div>
</div>
</div>
);
}
}
export default Faq;