The Human Cell Atlas

The Human Cell Atlas Aviv Regev Sarah A Teichmann Eric S Lander Ido Amit Christophe Benoist Ewan Birney Bernd Bodenmiller Peter Campbell Piero Carninci Menna Clatworthy Hans Clevers Bart Deplancke Ian Dunham James Eberwine Roland Eils Wolfgang Enard Andrew Farmer Lars Fugger Berthold Göttgens Nir Hacohen Muzlifah Haniffa Martin Hemberg Seung Kim Paul Klenerman Arnold Kriegstein Ed Lein Sten Linnarsson Emma Lundberg Joakim Lundeberg Partha Majumder John C Marioni Miriam Merad Musa Mhlanga Martijn Nawijn Mihai Netea Garry Nolan Dana Pe'er Anthony Phillipakis Chris P Ponting Stephen Quake Wolf Reik Orit Rozenblatt-Rosen Joshua Sanes Rahul Satija Ton N Schumacher Alex Shalek Ehud Shapiro Padmanee Sharma Jay W Shin Oliver Stegle Michael Stratton Michael J T Stubbington Fabian J Theis Matthias Uhlen Alexander van Oudenaarden Allon Wagner Fiona Watt Jonathan Weissman Barbara Wold Ramnik Xavier Nir Yosef Human Cell Atlas Meeting Participants

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The Human Cell Atlas 2017 eLife 10.7554/elife.27041 regev2017-the-human-cell-atlas regev2017-the-human-cell-atlas.txt, the project's staged copy c42041cd7d12c1440a16cea5e6bb7d1e4bdfc027 cc-by biology

the paper's own words

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0 spans located by searching the stored text for the quote's exact words, allowing any whitespace between them the human cell types themselves - a reference atlas defining them by molecular profile and connecting that to classical description Quotation withheld because this record is not cleared for redistribution. whether all human cell types can be identified and defined by molecular profile, 150 years after the effort began Quotation withheld because this record is not cleared for redistribution. a design for a comprehensive cell atlas WHICH DECLINES TO DEFINE ITS OWN CENTRAL TERM: the definition of 'cell type' is deferred to empirical observation on purpose, and the reasons are stated Quotation withheld because this record is not cleared for redistribution. method Quotation withheld because this record is not cleared for redistribution. cells as points in a high-dimensional molecular space, where similar cells are close but never identical Quotation withheld because this record is not cleared for redistribution. review review Quotation withheld because this record is not cleared for redistribution. a cell TYPE is proposed as a REGION or a PROBABILITY DISTRIBUTION in the full-dimensional molecular space or a projection of it - the category becomes a geometry rather than a list of properties Quotation withheld because this record is not cleared for redistribution. types discovered as regions in feature space are then to be DISTILLED into simple molecular and morphological signatures, so that independent laboratories can index and compare cells at all Quotation withheld because this record is not cleared for redistribution. THE PROJECT DECLINES TO DEFINE ITS CENTRAL TERM AND SAYS SO: `we have not attempted to propose a precise definition of 'cell type'. Rather, the definition should evolve based on empirical observation` - in a paper whose stated aim is to define all human cell types Quotation withheld because this record is not cleared for redistribution. the field lacks a rigorous definition of BOTH `cell type` and `cell state`, and the boundary between them is blurred because cells change over time in ways not fully understood Quotation withheld because this record is not cleared for redistribution. THE TAXONOMY MAY NOT BE A TAXONOMY: finer distinctions may not obey a strict hierarchy, some distinctions are graded rather than discrete, and IT REMAINS UNCLEAR WHETHER THE MORPHOLOGICAL, MOLECULAR AND PHYSIOLOGICAL AXES AGREE WITH EACH OTHER Quotation withheld because this record is not cleared for redistribution. the existing molecular classification is AD HOC - built on markers discovered by accident or chosen for convenience rather than systematically Quotation withheld because this record is not cleared for redistribution. clustering supplies only a starting framework: the `right` features, the `right` similarity metric and the `right` level of granularity are all open, and the paper puts each of the three in scare quotes Quotation withheld because this record is not cleared for redistribution. the full lineage tree from zygote to adult is known for exactly one organism - C. elegans, transparent, with about 1,000 cells Quotation withheld because this record is not cleared for redistribution. the definition of 'cell type' is deferred to empirical observation rather than fixed in advance, and the deferral is stated as a decision with its reasons eliminates: a catalogue whose categories were settled before the data that was supposed to produce them - and the paper's own reasons are that the hierarchy may not hold, the distinctions may be graded, and the axes may not agree · outcome: held Quotation withheld because this record is not cleared for redistribution. types found as regions in feature space must be distilled into signatures that independent laboratories can apply eliminates: a taxonomy that exists only inside the clustering run that produced it and cannot be used to index, aggregate or compare across labs and individuals · outcome: held Quotation withheld because this record is not cleared for redistribution. cell type cell type Quotation withheld because this record is not cleared for redistribution. cell state cell state Quotation withheld because this record is not cleared for redistribution. Cell-type taxonomies Cell-type taxonomies Quotation withheld because this record is not cleared for redistribution. markers markers Quotation withheld because this record is not cleared for redistribution. Cell Theory Cell Theory Quotation withheld because this record is not cleared for redistribution. scRNA-seq scRNA-seq Quotation withheld because this record is not cleared for redistribution. Human Cell Atlas Human Cell Atlas Quotation withheld because this record is not cleared for redistribution. comprehensive reference catalog comprehensive reference catalog Quotation withheld because this record is not cleared for redistribution. stable properties stable properties Quotation withheld because this record is not cleared for redistribution. transient features transient features Quotation withheld because this record is not cleared for redistribution. locations locations Quotation withheld because this record is not cleared for redistribution. abundances abundances Quotation withheld because this record is not cleared for redistribution. map map Quotation withheld because this record is not cleared for redistribution. relationships relationships Quotation withheld because this record is not cleared for redistribution. fundamental processes fundamental processes Quotation withheld because this record is not cleared for redistribution. system of coordinates system of coordinates Quotation withheld because this record is not cleared for redistribution. human cell human cell Quotation withheld because this record is not cleared for redistribution. defined set of molecular markers defined set of molecular markers Quotation withheld because this record is not cleared for redistribution. expression level expression level Quotation withheld because this record is not cleared for redistribution. 20,000 human protein-coding genes 20,000 human protein-coding genes Quotation withheld because this record is not cleared for redistribution. point in ~20,000-dimensional space point in ~20,000-dimensional space Quotation withheld because this record is not cleared for redistribution. non-coding genes non-coding genes Quotation withheld because this record is not cleared for redistribution. alternatively spliced forms alternatively spliced forms Quotation withheld because this record is not cleared for redistribution. chromatin state chromatin state Quotation withheld because this record is not cleared for redistribution. promoter and enhancer promoter and enhancer Quotation withheld because this record is not cleared for redistribution. post-translationally modified form post-translationally modified form Quotation withheld because this record is not cleared for redistribution. reduced representations reduced representations Quotation withheld because this record is not cleared for redistribution. histological and anatomical information histological and anatomical information Quotation withheld because this record is not cleared for redistribution. temporal information temporal information Quotation withheld because this record is not cleared for redistribution. disease status disease status Quotation withheld because this record is not cleared for redistribution. molecular profiles molecular profiles Quotation withheld because this record is not cleared for redistribution. Single-cell multi-omics Single-cell multi-omics Quotation withheld because this record is not cleared for redistribution. transcriptomic transcriptomic Quotation withheld because this record is not cleared for redistribution. genomic genomic Quotation withheld because this record is not cleared for redistribution. epigenomic epigenomic Quotation withheld because this record is not cleared for redistribution. proteomic proteomic Quotation withheld because this record is not cleared for redistribution. causal chains causal chains Quotation withheld because this record is not cleared for redistribution. genetic variation genetic variation Quotation withheld because this record is not cleared for redistribution. regulatory mechanisms regulatory mechanisms Quotation withheld because this record is not cleared for redistribution. phenotypic outcome phenotypic outcome Quotation withheld because this record is not cleared for redistribution. Multiplex in situ analysis Multiplex in situ analysis Quotation withheld because this record is not cleared for redistribution. spatial techniques spatial techniques Quotation withheld because this record is not cleared for redistribution. nucleic acids nucleic acids Quotation withheld because this record is not cleared for redistribution. proteins proteins Quotation withheld because this record is not cleared for redistribution. hybridization hybridization Quotation withheld because this record is not cleared for redistribution. antibody staining antibody staining Quotation withheld because this record is not cleared for redistribution. sequencing sequencing Quotation withheld because this record is not cleared for redistribution. tagging strategies tagging strategies Quotation withheld because this record is not cleared for redistribution. dissociated cells dissociated cells Quotation withheld because this record is not cleared for redistribution. spatial relationships spatial relationships Quotation withheld because this record is not cleared for redistribution. cell-cell communication cell-cell communication Quotation withheld because this record is not cleared for redistribution. MERFISH MERFISH Quotation withheld because this record is not cleared for redistribution. Seq-FISH Seq-FISH Quotation withheld because this record is not cleared for redistribution. microscopy-based quantification microscopy-based quantification Quotation withheld because this record is not cleared for redistribution. Imaging Mass Cytometry Imaging Mass Cytometry Quotation withheld because this record is not cleared for redistribution. tissue clearing tissue clearing Quotation withheld because this record is not cleared for redistribution. expansion expansion Quotation withheld because this record is not cleared for redistribution. Histology Histology Quotation withheld because this record is not cleared for redistribution. tissue architecture tissue architecture Quotation withheld because this record is not cleared for redistribution. expression signatures expression signatures Quotation withheld because this record is not cleared for redistribution. multi-gene signatures multi-gene signatures Quotation withheld because this record is not cleared for redistribution. cell's molecular profile cell's molecular profile Quotation withheld because this record is not cleared for redistribution. information about its neighborhood information about its neighborhood Quotation withheld because this record is not cleared for redistribution. absolute coordinates absolute coordinates Quotation withheld because this record is not cleared for redistribution. relative terms relative terms Quotation withheld because this record is not cleared for redistribution. machine vision machine vision Quotation withheld because this record is not cleared for redistribution. development development Quotation withheld because this record is not cleared for redistribution. partly asynchronous branching pathways of development partly asynchronous branching pathways of development Quotation withheld because this record is not cleared for redistribution. molecular changes molecular changes Quotation withheld because this record is not cleared for redistribution. gene-expression patterns gene-expression patterns Quotation withheld because this record is not cleared for redistribution. trajectories in high-dimensional space trajectories in high-dimensional space Quotation withheld because this record is not cleared for redistribution. Waddington's landscape Waddington's landscape Quotation withheld because this record is not cleared for redistribution. sharp transitions sharp transitions Quotation withheld because this record is not cleared for redistribution. sampling density sampling density Quotation withheld because this record is not cleared for redistribution. sorting strategies sorting strategies Quotation withheld because this record is not cleared for redistribution. rare, transient populations rare, transient populations Quotation withheld because this record is not cleared for redistribution. relative proportions of cells relative proportions of cells Quotation withheld because this record is not cleared for redistribution. duration of each phase duration of each phase Quotation withheld because this record is not cleared for redistribution. progenitor cells progenitor cells Quotation withheld because this record is not cleared for redistribution. rate of cell proliferation rate of cell proliferation Quotation withheld because this record is not cleared for redistribution. death death Quotation withheld because this record is not cleared for redistribution. true lineage trees true lineage trees Quotation withheld because this record is not cleared for redistribution. common progenitor cell type common progenitor cell type Quotation withheld because this record is not cleared for redistribution. synthetic circuits synthetic circuits Quotation withheld because this record is not cleared for redistribution. molecular barcode molecular barcode Quotation withheld because this record is not cleared for redistribution. lineage barcodes lineage barcodes Quotation withheld because this record is not cleared for redistribution. VDJ recombination VDJ recombination Quotation withheld because this record is not cleared for redistribution. somatic hypermutation somatic hypermutation Quotation withheld because this record is not cleared for redistribution. lineage tracing lineage tracing Quotation withheld because this record is not cleared for redistribution. somatic point mutations somatic point mutations Quotation withheld because this record is not cleared for redistribution. repeat expansions at microsatellite loci repeat expansions at microsatellite loci Quotation withheld because this record is not cleared for redistribution. sound statistical sampling sound statistical sampling Quotation withheld because this record is not cleared for redistribution. biological enrichment purification biological enrichment purification Quotation withheld because this record is not cleared for redistribution. adaptive, iterative approach adaptive, iterative approach Quotation withheld because this record is not cleared for redistribution. initial sparse sampling initial sparse sampling Quotation withheld because this record is not cleared for redistribution. decisions about further sampling decisions about further sampling Quotation withheld because this record is not cleared for redistribution. Sky Dive Sky Dive Quotation withheld because this record is not cleared for redistribution. banking banking Quotation withheld because this record is not cleared for redistribution. fixed or frozen tissues fixed or frozen tissues Quotation withheld because this record is not cleared for redistribution. mixed strategy mixed strategy Quotation withheld because this record is not cleared for redistribution. low coverage of the transcriptome low coverage of the transcriptome Quotation withheld because this record is not cleared for redistribution. deep profiles deep profiles Quotation withheld because this record is not cleared for redistribution. large-scale uniform sampling large-scale uniform sampling Quotation withheld because this record is not cleared for redistribution. stratified sampling stratified sampling Quotation withheld because this record is not cleared for redistribution. specialized sampling specialized sampling Quotation withheld because this record is not cleared for redistribution. atlas atlas Quotation withheld because this record is not cleared for redistribution. cellular branch cellular branch Quotation withheld because this record is not cleared for redistribution. spatial branch spatial branch Quotation withheld because this record is not cleared for redistribution. massively parallel transcriptome analysis massively parallel transcriptome analysis Quotation withheld because this record is not cleared for redistribution. chromatin chromatin Quotation withheld because this record is not cleared for redistribution. genome folding genome folding Quotation withheld because this record is not cleared for redistribution. somatic mutations somatic mutations Quotation withheld because this record is not cleared for redistribution. preserved tissue specimens preserved tissue specimens Quotation withheld because this record is not cleared for redistribution. 10 billion cells 10 billion cells Quotation withheld because this record is not cleared for redistribution. all tissues, organs, and systems all tissues, organs, and systems Quotation withheld because this record is not cleared for redistribution. world's diversity world's diversity Quotation withheld because this record is not cleared for redistribution. rarity of cell types/states rarity of cell types/states Quotation withheld because this record is not cleared for redistribution. spatial resolution spatial resolution Quotation withheld because this record is not cleared for redistribution. coverage of disease and diversity coverage of disease and diversity Quotation withheld because this record is not cleared for redistribution. functional assessment functional assessment Quotation withheld because this record is not cleared for redistribution. model organism atlases model organism atlases Quotation withheld because this record is not cleared for redistribution. engineering animals engineering animals Quotation withheld because this record is not cleared for redistribution. validation and functional follow-up studies validation and functional follow-up studies Quotation withheld because this record is not cleared for redistribution. by proxy by proxy Quotation withheld because this record is not cleared for redistribution. technically reproducible technically reproducible Quotation withheld because this record is not cleared for redistribution. biological variation biological variation Quotation withheld because this record is not cleared for redistribution. measurement noise measurement noise Quotation withheld because this record is not cleared for redistribution. rigorous protocols, standards, and benchmarks rigorous protocols, standards, and benchmarks Quotation withheld because this record is not cleared for redistribution. clinical annotations clinical annotations Quotation withheld because this record is not cleared for redistribution. consistent meta-data consistent meta-data Quotation withheld because this record is not cleared for redistribution. dissociating samples into single cells dissociating samples into single cells Quotation withheld because this record is not cleared for redistribution. fixation fixation Quotation withheld because this record is not cleared for redistribution. freezing freezing Quotation withheld because this record is not cleared for redistribution. validated standard operating procedures validated standard operating procedures Quotation withheld because this record is not cleared for redistribution. computational pipelines computational pipelines Quotation withheld because this record is not cleared for redistribution. benchmarking samples and data sets benchmarking samples and data sets Quotation withheld because this record is not cleared for redistribution. open data open data Quotation withheld because this record is not cleared for redistribution. standard models standard models Quotation withheld because this record is not cleared for redistribution. identifiable identifiable Quotation withheld because this record is not cleared for redistribution. data platforms data platforms Quotation withheld because this record is not cleared for redistribution. efficient aggregation and storage efficient aggregation and storage Quotation withheld because this record is not cleared for redistribution. quality control quality control Quotation withheld because this record is not cleared for redistribution. analytical software analytical software Quotation withheld because this record is not cleared for redistribution. user-friendly portals user-friendly portals Quotation withheld because this record is not cleared for redistribution. intellectually and technologically flexible intellectually and technologically flexible Quotation withheld because this record is not cleared for redistribution. criteria for 'completion' criteria for 'completion' Quotation withheld because this record is not cleared for redistribution. Human Cell Atlas → relationships The atlas shows relationships among catalogued elements. Shows is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. duration of each phase → relative proportions of cells Relative cell proportions convey information about the duration of each phase. Conveys-information-about is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. development → trajectories in high-dimensional space The paper proposes reconstructing development as trajectories in molecular space. Reconstructs-as is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. Single-cell multi-omics → causal chains Multi-omic measurements could help fill in causal chains. Enables is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. dissociated cells → tissue samples In-situ results map genomic information from dissociated cells back onto tissue samples. Maps-onto is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. expression data → absolute coordinates Cell expression data can help map cell position in absolute coordinates. Maps-position is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. low coverage of the transcriptome → cell types Low-coverage transcriptomes can identify many cell types reliably. Identifies is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. adaptive, iterative approach → Sky Dive The adaptive approach is explicitly termed a Sky Dive. Naming is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. deep profiles → low-coverage data A smaller set of deep profiles helps interpret the broad low-coverage data. Helps-interpret is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. preserved tissue specimens → analyzed later Preserved specimens allow collection now and analysis after methods mature. Enables-deferred-analysis is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. validation and functional follow-up studies → conclusions drawn in the human atlas Model-organism studies help validate human-atlas conclusions by proxy. Validates-by-proxy is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. data platforms → efficient aggregation and storage Atlas data platforms must provide aggregation and storage. Provides is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. standard models → identifiable Mapping sequence data onto standard gene models is proposed to mitigate identifiability. Mitigates is absent from the eight governed types. Quotation withheld because this record is not cleared for redistribution. cell type - DELIBERATELY UNDEFINED HERE. Proposed as a region or probability distribution in molecular space, described as intuitively compelling and hard to state precisely, and left to evolve from the data Quotation withheld because this record is not cleared for redistribution. cell type against cell state - type implies PERSISTENCE (a hepatic stellate cell), state implies TRANSIENCE (the G1 phase), and the paper says the boundary between the two concepts can be blurred Quotation withheld because this record is not cleared for redistribution. Cell-type taxonomies - a hierarchy over morphological, physiological and molecular differences, which the paper says may not be strict and whose three axes may not agree with one another Quotation withheld because this record is not cleared for redistribution. `scRNA-seq` - A NAME FOR A CLASS, NOT A PROTOCOL, AND THE PAPER SAYS SO IN ITS DEFINING SENTENCE. `Quotation withheld` Two papers both reporting `scRNA-seq` may share no step of their procedure - the review goes straight on to distinguish methods taking a census of mRNA at the 3' or 5' end from those assessing full transcripts. The term is a citation-level abstraction that is never a method-level one. Quotation withheld because this record is not cleared for redistribution. `Cell Theory` - A THEORY DEFINED AS THREE CONJOINED CLAIMS, TWO STRUCTURAL AND ONE HISTORICAL. `Quotation withheld.` The first two say what a thing IS MADE OF and what the parts DO; the third is a claim about ORIGIN and is the only one that could have been false without the others failing with it. A citation to `Cell Theory` selects one of the three and the name records which no better than a coin. Quotation withheld because this record is not cleared for redistribution. Human Cell Atlas - a relational map and reference catalog of cell properties, features, locations, and abundances Quotation withheld because this record is not cleared for redistribution. Atlas coordinate system - molecular dimensions plus anatomical, temporal, and disease annotations that can be collapsed into application-specific views Quotation withheld because this record is not cleared for redistribution. Single-cell multi-omics - two or more molecular data types measured in the same cell to connect variation, regulation, and phenotype Quotation withheld because this record is not cleared for redistribution. Multiplex in-situ analysis - selected RNA or protein targets measured inside tissue so dissociated-cell profiles can be mapped back into spatial context Quotation withheld because this record is not cleared for redistribution. Developmental trajectory - branching paths in high-dimensional molecular space reconstructed from cross-sectional single-cell observations Quotation withheld because this record is not cleared for redistribution. Lineage tracing - ancestry inferred from engineered or naturally accumulated molecular barcodes Quotation withheld because this record is not cleared for redistribution. Sky Dive - adaptive sampling that moves from uniform to stratified to specialized sampling while increasing resolution Quotation withheld because this record is not cleared for redistribution. Two-branch atlas - individual-cell molecular profiling paired with in-situ spatial mapping of tissue organization Quotation withheld because this record is not cleared for redistribution. Full-atlas scope - at least ten billion cells across tissues, organs, systems, health states, and population diversity, with explicit resolution and functional limits Quotation withheld because this record is not cleared for redistribution. Atlas quality - reproducibility through shared protocols, metadata, tissue handling, pipelines, and benchmarking materials Quotation withheld because this record is not cleared for redistribution. Open-data infrastructure - aggregation, storage, quality control, analysis software, and portals under participant and legal constraints Quotation withheld because this record is not cleared for redistribution. critiques → the existing molecular classification of cells, on the ground that it is ad hoc - built on markers discovered by accident or chosen for convenience Quotation withheld because this record is not cleared for redistribution. extends → Cell Theory as settled between 1838 and 1855, which named the cell as the unit and left the catalogue of kinds open for 150 years Quotation withheld because this record is not cleared for redistribution. cell state —distinct-from→ cell type cell state cell type differs in: persistence against transience - and the paper says the boundary is blurred · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): persistence against transience - and the paper says the boundary is blurred · the relation stated: type implies PERSISTENCE and state implies TRANSIENCE - and the paper says in the same passage that the boundary between the two CAN BE BLURRED, so the distinction is asserted and qualified together Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says the boundaries between cell type and cell state CAN BE BLURRED; distinct-from is hedged. Quotation withheld because this record is not cleared for redistribution. comprehensive reference catalog —part-of→ Human Cell Atlas comprehensive reference catalog Human Cell Atlas the relation itself is separately evidenced · strength of the relation: 1 · note: The atlas must include the comprehensive reference catalog. Quotation withheld because this record is not cleared for redistribution. human cell —operationalised-as→ point in ~20,000-dimensional space human cell point in ~20,000-dimensional space the relation itself is separately evidenced · strength of the relation: 0.7 · note: The paper proposes representing each cell as a point whose dimensions are gene-expression levels. Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says ONE MIGHT describe each cell as such a point; a proposal, hedged. Quotation withheld because this record is not cleared for redistribution. initial sparse sampling —causes→ decisions about further sampling initial sparse sampling decisions about further sampling direction on the measure: increases · the relation itself is separately evidenced · strength of the relation: 1 · note: The paper says initial sparse sampling drives later sampling decisions. Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says an adaptive approach is LIKELY beneficial, with sparse sampling driving later sampling; hedged. Quotation withheld because this record is not cleared for redistribution. cellular branch —part-of→ atlas cellular branch atlas the relation itself is separately evidenced · strength of the relation: 1 · note: The atlas must combine a cellular and a spatial branch. Quotation withheld because this record is not cleared for redistribution. spatial branch —part-of→ atlas spatial branch atlas the relation itself is separately evidenced · strength of the relation: 1 · note: The atlas must combine a cellular and a spatial branch. Quotation withheld because this record is not cleared for redistribution. the project does not propose a precise definition of 'cell type' and lets the definition evolve with empirical observation the project does not propose a precise definition of 'cell type' and lets the definition evolve with empirical observation Quotation withheld because this record is not cleared for redistribution. the cell-type hierarchy may not be strict, some distinctions are GRADED AND NOT DISCRETE, and it is unclear whether the morphological, molecular and physiological axes agree with each other the cell-type hierarchy may not be strict, some distinctions are GRADED AND NOT DISCRETE, and it is unclear whether the morphological, molecular and physiological axes agree with each other Quotation withheld because this record is not cleared for redistribution. molecular classification of cells has been AD HOC - markers discovered by accident or chosen for convenience rather than systematically molecular classification of cells has been AD HOC - markers discovered by accident or chosen for convenience rather than systematically Quotation withheld because this record is not cleared for redistribution. the `right` features, the `right` similarity metric and the `right` granularity are all open problems, and the paper scare-quotes each of the three the `right` features, the `right` similarity metric and the `right` granularity are all open problems, and the paper scare-quotes each of the three Quotation withheld because this record is not cleared for redistribution. the full lineage tree from zygote to adult is known for one organism only - C. elegans, with about 1,000 cells the full lineage tree from zygote to adult is known for one organism only - C. elegans, with about 1,000 cells Quotation withheld because this record is not cleared for redistribution. a region or a probability distribution in the full-dimensional molecular space or a projection of it - offered as intuitively compelling and explicitly NOT as a precise definition cell type Quotation withheld because this record is not cleared for redistribution. all organisms are composed of one or more cells; cells are the basic unit of structure and function in life; all cells are derived from pre-existing cells Cell Theory Quotation withheld because this record is not cleared for redistribution. an international effort to define all human cell types by distinctive molecular profile and connect that to classical descriptions such as location and morphology the Human Cell Atlas Quotation withheld because this record is not cleared for redistribution. years - the age of the effort to identify all human cell types, which this project proposes to complete 150 Quotation withheld because this record is not cleared for redistribution. cells in C. elegans - the only organism whose full lineage tree from zygote to adult is known 1000 Quotation withheld because this record is not cleared for redistribution. the years in which Schleiden, Schwann, Remak and Virchow crystallised Cell Theory 1838-1855 Quotation withheld because this record is not cleared for redistribution. probability distribution probability distribution Quotation withheld because this record is not cleared for redistribution. granularity granularity Quotation withheld because this record is not cleared for redistribution. similarity metric similarity metric Quotation withheld because this record is not cleared for redistribution. molecular profiles molecular profiles Quotation withheld because this record is not cleared for redistribution.

The full text of this article is not redistributable, so it is not included here. The evidence sentences are withheld with it; the tag layer and its grounding status remain. The article itself is at https://doi.org/10.7554/elife.27041.