# A shared annotation tool helped create a cell atlas Markdown copy of https://realalpha.app/s/a-shared-annotation-tool-helped-create-a-cell-atlas/ on Real Alpha, the best minutes from long interviews with the people building AI. Cite and link the page, not this copy. - Speaker: [Priscilla Chan](https://realalpha.app/people/priscilla-chan/) · Chan Zuckerberg Initiative - Host: [Erik Torenberg](https://realalpha.app/people/erik-torenberg/) · General partner, Andreessen Horowitz · Helped build Product Hunt; founded On Deck, Village Global and Turpentine. - Show: a16z Podcast - Episode: [Mark Zuckerberg & Priscilla Chan: How AI Will Cure All Disease](https://realalpha.app/v/YnV8pgHtO5Y/), Nov 6, 2025 - Moment: 15:18 to 18:34 of the episode (3 min), playing on https://realalpha.app/s/a-shared-annotation-tool-helped-create-a-cell-atlas/; the episode from there: https://realalpha.app/v/YnV8pgHtO5Y/?t=918 ## Quote > “We've only funded 25% of it. **75% came from the broader community** saying, this is useful and there's an easy way for us to standardize and build this together.” > — [Priscilla Chan](https://realalpha.app/people/priscilla-chan/) at [17:40](https://realalpha.app/v/YnV8pgHtO5Y/?t=1060) · a16z Podcast ## Takeaways 1. Cell by Gene began as a fix for slow data annotation. 2. A shared tool standardized data formats across labs. 3. The broader community contributed 75% of the atlas. ## About this segment Priscilla Chan and Zuckerberg describe how an annotation bottleneck led to Cell by Gene and a common data format. The community built most of the atlas, beyond what CZI funded. From “Mark Zuckerberg & Priscilla Chan: How AI Will Cure All Disease”, Nov 6, 2025. [Watch the full episode](https://realalpha.app/v/YnV8pgHtO5Y/) ## Transcript Transcribed by machine (Whisper) from the episode’s audio, so a word may be off here and there. [15:25](https://realalpha.app/v/YnV8pgHtO5Y/?t=925) Cell by gene is like almost an accident, though. Tell us more. So do you want to share a little bit about cell by gene, or do you want me to start? Well, I mean, I don't know which part you want to get into, but I mean, but the cell atlas work overall, and it's kind of this crazy thing that we're, you know, here in 2025, and there's not the kind of periodic table of elements equivalent for biology, right? [15:47](https://realalpha.app/v/YnV8pgHtO5Y/?t=947) So that was sort of a lot of the inspiration of it was, all right, how do we both through work that we're going to do in the biohub and through other grants, be able to pull together and standardize a format where you can have all this data? and when we We're starting off, we didn't even necessarily have in mind that we were going to use that to build virtual cell models. I think that's sort of just come into focus as the AI work has advanced, but that's a very exciting thing. [16:13](https://realalpha.app/v/YnV8pgHtO5Y/?t=973) We should definitely spend a bunch of time on the virtual cell models, but I'm not sure what you wanted to get into on the Cell Atlas. Well, the single-cell work was one of our first RFAs 10 years ago we started, and we were like, okay, we think this is possible. We actually funded the methodology for it to standardize how it was going to be done. So that was 10 years ago. And then we seeded a few labs to start building out that data set. [16:38](https://realalpha.app/v/YnV8pgHtO5Y/?t=998) But we were like, there are like millions or billions of different cell types and different permutations. Like, how are we going to do this? And especially with like a burgeoning technique. And so we ended up seeding a few groups and they started doing work. And then they told us they had a problem. There was a bottleneck in their workflow because they couldn't annotate the data fast enough. And so we built, Cell by Gene was an annotation tool. [17:08](https://realalpha.app/v/YnV8pgHtO5Y/?t=1028) That's the original source of this. So we built the annotation tool to make it easy for people who are doing single cell science to be able to annotate the data. And then we put the data that we collected publicly so people could share. But because everyone started using the same annotation tool, everyone was standardized then on the same data formats. And then there started being a community around the tool, and they wanted to share back and build the atlas. [17:35](https://realalpha.app/v/YnV8pgHtO5Y/?t=1055) So now after 10 years, there are millions of cells that have been built into this shared resource for the entire scientific community. We only funded about 75% of it. Sorry, that's wrong. We've only funded 25% of it. 75% came from the broader community saying, this is useful and there's an easy way for us to standardize and build this together. The same metadata. Yeah, that's right. It's like an interesting, what you'd call a network effect. [18:03](https://realalpha.app/v/YnV8pgHtO5Y/?t=1083) I was going to say, it sounds like the internet. Come for the annotation, stay for the virtual cell model. Well, it was very important when we were getting started with the work to have everyone who was doing it have a consistent format. So that way it could be used and portable. And then once that kind of took off as the way that it would get done, then other people just found it valuable. Yeah, and even relative to prior data bases like Geo and whatnot, they're just simply not as standardized or QC. [18:29](https://realalpha.app/v/YnV8pgHtO5Y/?t=1109) Yeah.