#OntoCode
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selfresearch.org
This is exactly why we built OntoCode. We need tooling capable of handling the extreme scale of biological graph alignment, natively in the browser.

The bottleneck in science isn't a lack of data. It is a lack of shared meaning.
September 25, 2026 at 4:38 PM
selfresearch.org
Your downstream pipeline shouldn't dictate how you do your science. 🧪

Want to try it out? Access the IDE beta here: [Insert Link]

#SemanticWeb #JSONLD #DataEngineering #Ontology #WebDev #Bioinformatics #OntoCode (3/3)
July 10, 2026 at 4:29 PM
selfresearch.org
‪Self Research Institute‬
‪@selfresearch.org‬
· 3d
Your downstream pipeline shouldn't dictate how you do your science. 🧪

Want to try it out? Access the IDE beta here: selfresearch.org/products/ont...

#SemanticWeb #JSONLD #DataEngineering #Ontology #WebDev #Bioinformatics #OntoCode (3/3)
July 13, 2026 at 6:12 PM
selfresearch.org
The Future of Ontology Engineering is Here 🚀🕸️

The OntoCode public beta is officially open! Whether you are an independent researcher or a company building precision health apps, it's time to leave legacy tooling behind.

#OntoCode #OpenSource #DigitalTwin
June 22, 2026 at 5:40 PM
selfresearch.org
We’ve been quiet lately because we are obsessed with speed. ⏱️

Legacy tools stall when merging heavy environmental/biological ontologies. We just benchmarked #OntoCode merging over 159k axioms in 11.89s.

Less loading screens. More science. Keep an eye out for our upcoming IDE.

#BuildInPublic
A graphic highlighting OntoCode's performance. The headline reads, "Theory ➔ Executable Model. Over 159,000 axioms cleanly merged in 11.89 seconds. The path just got significantly shorter." Below is a software UI showing a successful "Merge Ontologies" workflow, combining source file ecto.owl with target file envo(2).owl. A green checkmark indicates success, and a hand-drawn blue arrow points to the merge statistics: "Axioms Added: 159862" and "Duration: 11.89s." The Self Research Institute logo is at the bottom right.
May 29, 2026 at 5:24 PM
selfresearch.org
Get started or contribute:

📦 VS Code: marketplace.visualstudio.com/items?itemNa...
⭐ GitHub: github.com/The-Self-Res...

#SemanticWeb #Ontology #VSCode #OpenSource #DevTools
OntoCode Studio - Visual Studio Marketplace
Extension for Visual Studio Code - Edit OWL files with authentication and web-based interface
marketplace.visualstudio.com
August 17, 2026 at 7:51 PM
selfresearch.org
Modeling the body isn't just plumbing — it's about context. 🧬

A data point only means something when you can trace it back to the evidence. Capturing multiscale biological logic takes a verifiable link between your code and the literature.

#OntoCode #SystemsBiology
An infographic titled "Modeling the body isn't plumbing. It's context." Above the title, small text reads "ONTOCODE • CONTEXT, NOT JUST PLUMBING". The central image shows a dark-themed code editor displaying ontology code in the background, overlaid with an "Insert Citation" modal. The modal displays a search interface connected to a Zotero library, listing academic references related to "Standards of Care in Diabetes—2026". Below the screenshot, text reads, "Blood pressure reacts to environmental load — so OntoCode brings Zotero into the IDE, keeping every semantic relationship verifiable against the literature." The Self Research Institute logo and website URL are in the footer.
June 12, 2026 at 6:46 PM
selfresearch.org
Does your lab’s version control look like cell_type_FINAL_v3.owl?

OntoCode lives natively inside VS Code. Every ontology edit becomes a clean, standard Git diff. Submit PRs and collaborate without the chaos. 🧬

Jump into the open-source beta: selfresearch.org/products/ont...
A promotional graphic by the Self Research Institute for OntoCode, highlighting Git-native ontologies. The headline reads, "If _FINAL_v3.owl is your version control, we need to talk." The subtext adds, "OntoCode lives in the VS Code ecosystem, so every edit is a clean, standard Git diff — pull requests, deprecation tracking, real collaboration." The image compares two workflows. On the left, "THE OLD WAY" shows a messy list of file names including cell_type_FINAL.owl, cell_type_FINAL_v3.owl, and cell_type_USE_THIS.owl, with a warning at the bottom stating, "which one is current? nobody knows." On the right, "IN ONTOCODE" displays a modern, dark-mode code editor showing a clean Git diff for cell_type.owl. A deprecated label for "nerve cell" is highlighted in red as removed, while the updated "Neuron" label is highlighted in green as added. The bottom of the editor shows standard Git status markers like "PR #42", "2 reviewers", and "git: main". A teal button at the bottom reads "JOIN THE OPEN-SOURCE BETA. Collaborate without the chaos — link in bio.”
September 11, 2026 at 4:15 PM
selfresearch.org
Whether modeling clinical pathways or mapping aerospace supply chains, the architecture is the same. You are querying a network of meaning, not a spreadsheet. 🌐

We built OntoCode to give you the IDE to build and query these relationships. 🛠️ #SPARQL #KnowledgeGraphs
September 4, 2026 at 4:42 PM
selfresearch.org
Update: We can now officially share our VS Code extension and GitHub repo.

If you are working with ontologies or semantic architecture, we would love for you to test it out and collaborate with us.

VS Code: marketplace.visualstudio.com/items?itemNa...
GitHub: github.com/The-Self-Res...
OntoCode Studio - Visual Studio Marketplace
Extension for Visual Studio Code - Edit OWL files with authentication and web-based interface
marketplace.visualstudio.com
September 4, 2026 at 4:46 PM
selfresearch.org
That structured meaning is how an ontology answers complex questions that a flat spreadsheet structurally can't.

We build OntoCode for people who want to model meaning, not just store it. 🛠️

#Ontology #KnowledgeGraphs #DataModeling #HealthTech
August 28, 2026 at 4:47 PM
selfresearch.org
Excited to launch the open beta of OntoCode by @selfresearch.org!

A microservice-driven platform for real-time OWL ontology editing, multi-reasoner execution (HermiT, ELK, Pellet), & D3.js graph visualization.

Try our 14-day open access trial:
selfresearch.org/products/ont...
The Self Research Institute
Human computation and personal informatics research and software development.
selfresearch.org
August 17, 2026 at 7:51 PM
selfresearch.org
Refactoring code is scary. Refactoring a 10,000-node biological ontology is terrifying. Change one entity, and it cascades to break hundreds of relationships silently. 🧬💥

Enter OntoCode: IDE-grade tooling for semantic webs.

Try it now: lnkd.in/g3XuTqJK 🧵👇
Infographic titled 'IDE-Grade Tooling for Semantic Webs: Change one entity — the reasoner tells you what broke' by Self Research Institute. The graphic displays an ontology editor interface where editing the molecule 'ATP' automatically triggers a reasoner to flag the dependent process 'GlycolysisStep' as an unsatisfiable class. A bottom banner reads 'Refactor with confidence' alongside a 'Try The Beta' button.
July 29, 2026 at 5:01 PM
selfresearch.org
Get your identifiers right and labels can evolve freely without breaking things downstream. Stable IDs are the quiet foundation of interoperable science.

Test our Ontology editor in beta: selfresearch.org/ontocode-sub...
Coming Soon
Human computation and personal informatics research and software development.
selfresearch.org
July 27, 2026 at 6:31 PM
selfresearch.org
You almost never need to model biology from zero. Reusing established OBO standards (HPO, GO, Uberon, CL) keeps data interoperable.

We built OntoCode as an ontology editor to extend existing standards seamlessly.

Register for our Beta: selfresearch.org/ontocode-sub...

#TechBio
Infographic titled 'Stand on the shoulders of the ontologies that came before' by Self Research Institute. It illustrates how a custom ontology model sits on top of existing OBO Foundry standards: HPO (Phenotypes), GO (Gene function), Uberon (Anatomy), and CL (Cell types). A callout box reads 'Align to what exists, extend only where you must — and keep your model interoperable by design' next to an 'Explore The Beta' button.
July 24, 2026 at 4:36 PM
selfresearch.org
What will you build this week? It’s been an incredible week for OntoCode & Sci2Code. Huge thanks to everyone registered to test the beta!

Import an OWL file, visualize your mesh, and eliminate citation debt: selfresearch.org/ontocode-sub...
The era of Biological Alignment starts at the code level.
July 20, 2026 at 8:17 PM
selfresearch.org
What is your biggest bottleneck when feeding data to LLMs? 👇

Sign up for our beta: selfresearch.org/ontocode-sub...

#GenerativeAI #GraphRAG #KnowledgeGraphs #DataEngineering #VSCode #SemanticWeb
July 17, 2026 at 5:04 PM
selfresearch.org
We talk about precision medicine, but human biology isn't fully computable yet. Spreadsheets can't map a complex physiological cascade.

Bridging macro symptoms to micro cellular data requires cross-domain knowledge graphs. That's why we built OntoCode.

Sign up: selfresearch.org/ontocode-sub...
A promotional graphic by the Self Research Institute for OntoCode titled "Macro-Micro Sync." The headline reads, "From symptom to cell, in one connected graph." The subtext explains, "You can't map a physiological cascade with flat spreadsheets. OntoCode links macro symptoms to micro cellular data through dynamic, cross-domain knowledge graphs." The center features a dark-mode network graph mapping a physiological cascade across three physical scales: Macro (organ, ~10 cm), Meso (tissue, ~1 mm), and Micro (molecule, ~1 nm). The nodes are color-coded by Phenotype, Anatomy, and Molecular domains. At the micro level, a molecular "TNNT2 variant" links to "Troponin T," which links upward to meso-level "Sarcomere" and "Cardiac muscle." These connect to the macro-level "Heart," which branches out to the phenotypic symptoms of "Chest pain" and "Fatigue.”
July 15, 2026 at 4:37 PM
selfresearch.org
Over 1M new biomedical papers hit PubMed every year. No curation team can read that by hand. 🌊

The bottleneck isn't expertise—it's tooling. We need to treat knowledge curation as an engineering problem, not manual entry.

Join the OntoCode beta: selfresearch.org/products/ont...

#Biocuration
Infographic titled 'By the Numbers' featuring a large '1M+' statistic. The main text reads: 'new biomedical papers are indexed in PubMed every year — far more than any curator can read by hand. The bottleneck isn’t effort. It’s tooling.' The graphic references a 2024 National Library of Medicine report on MEDLINE PubMed production statistics and includes the Self Research Institute logo.
July 13, 2026 at 6:14 PM
selfresearch.org
The gap between academia and modern tech is really just a gap between file formats. 📄➡️💻

Bio-curation leans on strict OWL. Web devs need JSON-LD. For years, bridging the two has meant maintaining brittle, error-prone custom conversion scripts between your ontology and your product. (1/3)
A promotional graphic by the Self Research Institute for OntoCode. The top tag reads, "ONTOCODE • ONE SOURCE, EVERY FORMAT." The main bold headline states, "Curate in OWL. Export to JSON-LD." The subtext explains, "Academia leans on strict OWL; web builders need JSON-LD. Curate once, then export to the serialization your pipeline expects — no manual conversion." The central graphic is a dark-mode user interface showing a "File > Export As..." menu. On the left, a source file named "SDA_Merged.ttl" is shown with the note, "One canonical model. Edit it once." An arrow points to a list of seven export formats on the right: .owl (RDF/XML) tagged for "LAB", .jsonld (JSON-LD) tagged for "WEB" and highlighted, .ttl (Turtle), .owlxml (OWL/XML), .omn (Manchester), .ofn (Functional), and .obo (OBO Flatfile). The bottom status bar reads "one source of truth | 7 export formats | no manual conversion." A teal call-to-action button at the bottom says, "ACCESS THE BETA → Export in the format that fits your pipeline — link in bio.”
July 10, 2026 at 4:29 PM
selfresearch.org
3/ It bridges academia & web dev. Researchers build models in strict OWL; developers need JSON. JSON-LD acts as the perfect translation layer.

We built OntoCode to let you curate in strict OWL and export to strict JSON-LD with a single click. Build infrastructure that actually scales. (3/3)
July 8, 2026 at 6:04 PM
selfresearch.org
💻 Desktop IDE (Uncapped Seats):
Runs locally on your machine. No caps—install, connect to your environment, and go.

Pick your workflow, but if you want the browser version, reserve your spot before allocation fills up!

👉 selfresearch.org/products/ont...

#OntoCode #SemanticWeb
July 6, 2026 at 5:38 PM
selfresearch.org
Beta registrations are open! 🕸️

We’re offering two ways to use our ontology editor, with one catch:

🌐 Browser Web App (Capped Seats):
Runs on our servers. We’re capping seats to guarantee a fast, stable experience. Once full, they're full. 🧵
An infographic by the Self Research Institute for the OntoCode Beta titled "Pick your seat before the weekend." The subtitle reads: "Web seats are capped to keep the browser version fast and stable. Desktop IDE seats are open — no cap." Below are two side-by-side option cards. The left card, "Browser version," features badges for "Limited" and "Capped Pool," explaining: "A fixed number of web seats, so we can watch server load and keep it snappy." The right card, "Desktop IDE," features badges for "Open" and "No Limit • Install Today," explaining: "Runs on your own machine, so seats stay wide open. Reserve and download anytime." A dark banner at the bottom reads "Reserve your version before the weekend" alongside a "Reserve Now" button.
July 6, 2026 at 5:38 PM
selfresearch.org
How much time do you lose cross-referencing ontology nodes with the papers that validate them? ⏳

OntoCode’s Sci2Code integration lets you pull citations from Zotero and embed them into your RDF code as you type. 💻

Test the beta:
👉 selfresearch.org/products/ont...

#OntoCode #Zotero
An infographic by the Self Research Institute for OntoCode's Sci2Code and Zotero integration. The main headline reads, "Search your library. Cite as you curate." The subtext explains, "Stop hand-matching nodes to the papers that validate them. Sci2Code searches your Zotero library and inserts verifiable, DOI-backed citations straight into your RDF." The visual is a mockup of a dark-mode code editor with a white "Insert Citation" modal overlaid. In the modal, a search for "heart" yields 23 matches. The top result highlights the journal article "Classification, ontologies, and precision medicine" by Haendel, Chute & Robinson (2018) from the New England Journal of Medicine, displaying its DOI link. A second result for a webpage notes, "No DOI — will prompt to add.”
July 3, 2026 at 5:00 PM
selfresearch.org
Open science requires secure, verified infrastructure. 🛡️ To get the official, GPLv3-protected OntoCode IDE—complete with CI/CD testing pipelines and Zotero integration— download directly from @selfresearch.org.

Register for the closed beta here:
👉 selfresearch.org/products/ont...
A launch day promotional graphic by the Self Research Institute. The header reads "LAUNCH DAY • VERIFIED RELEASE." The main bold headline states, "Get the genuine build — verified by the Self Research Institute," with the word "genuine" highlighted in teal. Below are two product cards for "Sci2Code" and "OntoCode," both displaying a green "VERIFIED" checkmark badge. Underneath are three feature tags with green checkmarks: "GPLv3-protected," "Full CI/CD test pipeline," and "Native Zotero integration." A central box with a blue shield icon is titled "DOWNLOAD ONLY FROM THE SOURCE." The text reads, "Use only the links on our official GitHub repository and selfresearch.org. The open-source community deserves secure, verified infrastructure." A dark navy call-to-action banner at the bottom says, "Get on the official waitlist," next to a teal "JOIN THE BETA →" button. The footer features the Self Research Institute logo and website.
June 29, 2026 at 6:04 PM