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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Tools & Services — FDI Lab</title>
<meta name="description" content="Software tools, ontologies, portals, and services developed and maintained by the FAIR Data Informatics Lab at UC San Diego.">
<link rel="stylesheet" href="css/style.css">
<style>
.tool-grid {
display: grid;
grid-template-columns: repeat(auto-fill, minmax(300px, 1fr));
gap: 1.25rem;
margin-top: 2rem;
}
.tool-card {
background: var(--white);
border-radius: 8px;
padding: 1.4rem 1.5rem;
border: 1px solid var(--gray-mid);
border-top: 4px solid var(--accent);
box-shadow: 0 2px 10px rgba(18,46,94,0.07);
display: flex;
flex-direction: column;
gap: 0.4rem;
}
.tool-card h3 {
font-size: 1.1rem;
margin: 0;
}
.tool-card .tool-type {
font-size: 0.78rem;
text-transform: uppercase;
letter-spacing: 0.06em;
font-weight: 700;
color: var(--accent);
}
.tool-card p {
font-size: 0.9rem;
color: var(--gray-text);
margin: 0;
flex: 1;
}
.tool-links {
display: flex;
align-items: center;
gap: 0.75rem;
flex-wrap: wrap;
margin-top: 0.5rem;
}
.tool-links a {
font-size: 0.85rem;
font-weight: 700;
}
.rrid-badge {
font-size: 0.75rem;
font-family: monospace;
background: var(--accent-light);
color: var(--navy);
padding: 0.15rem 0.45rem;
border-radius: 4px;
}
.section-label {
font-size: 1.25rem;
font-weight: 700;
color: var(--navy);
border-bottom: 2px solid var(--gray-mid);
padding-bottom: 0.4rem;
margin: 3rem 0 0;
}
@media (max-width: 640px) {
.tool-grid { grid-template-columns: 1fr; }
}
</style>
</head>
<body>
<header>
<div class="header-inner">
<a href="index.html" class="logo">
<img src="images/site/fdi-logo-white.png" alt="FDI Lab" style="height:36px; object-fit:contain;">
</a>
<button class="nav-toggle" onclick="document.querySelector('nav').classList.toggle('open')" aria-label="Toggle menu">
<span></span><span></span><span></span>
</button>
<nav>
<a href="index.html">Home</a>
<a href="about.html">About</a>
<a href="team.html">Team</a>
<div class="nav-dropdown">
<button class="nav-dropdown-btn active" onclick="this.closest('.nav-dropdown').classList.toggle('open')">Research ▾</button>
<div class="nav-dropdown-menu">
<a href="projects.html">Projects</a>
<a href="tools.html" class="active">Tools & Services</a>
<a href="funding.html">Funding</a>
<a href="publications.html">Publications</a>
</div>
</div>
<a href="contact.html">Contact</a>
</nav>
</div>
</header>
<div class="page-hero">
<div class="container">
<h1>Tools & Services</h1>
<p>Software platforms, ontologies, registries, and services developed and maintained by FDI Lab.</p>
</div>
</div>
<section>
<div class="container">
<h3 class="section-label">Platforms & Portals</h3>
<div class="tool-grid">
<div class="tool-card">
<div class="tool-type">Community Portal</div>
<h3>SciCrunch</h3>
<p>Community portal for researchers providing information on common sources of data and Research Resource Identifiers (RRIDs). Enables searching, creation, and discovery of research resources across multiple domains.</p>
<div class="tool-links">
<a href="https://scicrunch.org/" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_003115</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Resource Registry</div>
<h3>SciCrunch Resource Registry</h3>
<p>Interactive portal for finding and submitting biomedical resources. Resources receive RRIDs for citation in scientific manuscripts, making them findable and citable across the literature.</p>
<div class="tool-links">
<a href="https://scicrunch.org/scicrunch/about/sources/nlx_144509-1" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_005400</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Identifier System</div>
<h3>RRIDs Portal</h3>
<p>Central location for persistent, unique Research Resource Identifiers (RRIDs) for antibodies, model organisms, cell lines, and tools — supporting the Resource Identification Initiative across 800+ biomedical journals.</p>
<div class="tool-links">
<a href="https://scicrunch.org/resources" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_004098</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Antibody Resource</div>
<h3>Antibody Registry</h3>
<p>Specialized registry for antibody resources within the biomedical research ecosystem. Enables researchers to locate, identify, and cite specific antibody reagents with persistent identifiers.</p>
<div class="tool-links">
<a href="https://www.antibodyregistry.org/" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_006397</span>
</div>
</div>
</div>
<h3 class="section-label">Ontologies & Terminology</h3>
<div class="tool-grid">
<div class="tool-card">
<div class="tool-type">Biomedical Lexicon</div>
<h3>InterLex</h3>
<p>A dynamic lexicon of biomedical terms providing a federated ontology layer and inter-lexical mappings. Built on the NeuroLex foundation, it enables consistent terminology across biomedical databases and tools.</p>
<div class="tool-links">
<a href="http://interlex.org" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_016178</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Neuroscience Ontology</div>
<h3>NIF Ontology</h3>
<p>NIFSTD maintains an extensive set of terms and concepts important for the domains of neuroscience and biology. The ontology underpins resource discovery and data integration across the NIF ecosystem.</p>
<div class="tool-links">
<a href="https://github.com/SciCrunch/NIF-Ontology" target="_blank" rel="noopener">GitHub →</a>
<span class="rrid-badge">RRID: SCR_005414</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Neuron Phenotype Ontology</div>
<h3>Neuron Phenotype Ontology</h3>
<p>An ontology for describing the complex phenotypes of neurons, enabling consistent classification and comparison of neuronal cell types across datasets and research communities.</p>
<div class="tool-links">
<span class="rrid-badge">RRID: SCR_017403</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Resolution Service</div>
<h3>Resolver</h3>
<p>Resolution service supporting NIFSTD ontology term and concept lookup. Provides stable, resolvable URIs for ontology terms used across the NIF and SciCrunch infrastructure.</p>
<div class="tool-links">
<a href="https://scicrunch.org/resolver" target="_blank" rel="noopener">Visit →</a>
</div>
</div>
</div>
<h3 class="section-label">Software & APIs</h3>
<div class="tool-grid">
<div class="tool-card">
<div class="tool-type">Ontology Web Services</div>
<h3>SciGraph</h3>
<p>A turnkey solution for ontology web services that converts OWL ontologies into Neo4j graphs, providing API endpoints for autocomplete, terminology lookup, and graph traversal. Open source on GitHub.</p>
<div class="tool-links">
<a href="https://github.com/SciCrunch/SciGraph" target="_blank" rel="noopener">GitHub →</a>
<span class="rrid-badge">RRID: SCR_017576</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Information Integration</div>
<h3>DISCO</h3>
<p>An information integration approach designed to facilitate interoperation among Internet resources through harvesting and updating. DISCO enables federated search across heterogeneous biomedical data sources.</p>
<div class="tool-links">
<span class="rrid-badge">RRID: SCR_004586</span>
</div>
</div>
</div>
<h3 class="section-label">Analytics & Reporting</h3>
<div class="tool-grid">
<div class="tool-card">
<div class="tool-type">dkNET Service</div>
<h3>Resource Reports</h3>
<p>Provides a detailed overview of individual research resources including citation metrics, community feedback, and co-usage information. Helps researchers assess the impact and reliability of specific resources.</p>
<div class="tool-links">
<span class="rrid-badge">RRID: SCR_019227</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">dkNET Compliance Tool</div>
<h3>Authentication Reports</h3>
<p>An automated tool to enable researchers to create customized reports for NIH Submission Policy compliance regarding cell line and antibody authentication requirements.</p>
<div class="tool-links">
<span class="rrid-badge">RRID: SCR_019226</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Analytics Platform</div>
<h3>Resource Information Network</h3>
<p>An integrated dataset and analytics platform combining Research Resource Identifiers (RRIDs), text mining, and data aggregation to provide insight into resource usage across the biomedical literature.</p>
</div>
<div class="tool-card">
<div class="tool-type">Validation Knowledgebase</div>
<h3>Resource Watch</h3>
<p>Stores validation and problematic information about research resources, enabling researchers to submit F.A.I.R. claims and alert the community to issues with specific reagents or tools.</p>
<div class="tool-links">
<a href="https://scicrunch.org/ResourceWatch" target="_blank" rel="noopener">Visit →</a>
<span class="rrid-badge">RRID: SCR_021761</span>
</div>
</div>
<div class="tool-card">
<div class="tool-type">Text Mining Alert System</div>
<h3>Antibody Watch</h3>
<p>Automatically alerts researchers about problematic antibodies using deep neural networks to extract specificity statements from scientific literature, helping prevent the use of unreliable reagents.</p>
</div>
</div>
</div>
</section>
<footer>
<div class="footer-inner">
<div class="footer-links">
<a href="index.html">Home</a>
<a href="about.html">About</a>
<a href="team.html">Team</a>
<a href="projects.html">Projects</a>
<a href="tools.html">Tools & Services</a>
<a href="funding.html">Funding</a>
<a href="publications.html">Publications</a>
<a href="contact.html">Contact</a>
</div>
<div class="footer-github">
<a href="https://github.com/SciCrunch/FDI-Lab-Website" target="_blank" rel="noopener">
<img src="images/site/github-mark.svg" alt="">GitHub
</a>
<a href="https://github.com/SciCrunch/FDI-Lab-Website/issues/new" target="_blank" rel="noopener">
<img src="images/site/github-mark.svg" alt="">Leave feedback
</a>
</div>
<p>© <span id="yr"></span> FAIR Data Informatics Lab • UC San Diego</p>
</div>
</footer>
<script>document.getElementById('yr').textContent = new Date().getFullYear();</script>
</body>
</html>