The Large-Scale Organization of Metabolic Networks

H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, A.-L. Barabási · Nature / arXiv · 2000 · biology · 10.1038/35036627 · record jeong2000-metabolic-networks
tag layer · index · concepts · authors · עברית

Where this record's text came from. faceted 2026-08 by reading the locally held text (pdftext); every evidence string verified as an exact substring of that text before merging. method is labelled 'computational-network-analysis' - the study is graph-theoretic analysis of an existing pathway-genome database plus node-removal computer simulations ('To examine if metabolic networks display a similar error tolerance we performed computer simulations on the metabolic network of the bacterium, E. coli.'); 'simulation' alone would misdescribe the main analysis. The power-law result itself is stated as 'As illustrated in Fig. 2, Quotation withheld.' The 'contradicts' relation is anchored on the paper's own explicit contrast marker against the prior expectation it quotes: 'For all non-biological networks examined to date the average connectivity of a node is fixed, which implies that the diameter of a network increases logarithmically with the addition of new nodes 2, 27, 28.' replication status 'untested': the uniformity across 43 organisms is within-study generalisation, not independent replication; the paper notes agreement with prior mutagenesis studies but does not claim to replicate them. 2026-08-12 and 2026-08-15 schema-0.3 passes: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.

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Other fields define these differently the same word, defined another way in another discipline
standard-deviation 3 fields · connectivity 2 fields

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 13 concept tags on this paper, 11 are grounded in a quoted sentence. 9 carry the tagger's gloss of what the term means in this paper, which is not something the article can license.

scale-free network metabolic network network topology network hub node substrate link metabolic reactions exponential networks hubs network diameter biochemical pathway small-world character growth with preferential attachment: new nodes join by attaching to already well connected ones, which is what produces the power law hub dominance: a few highly connected substrates carry the connectivity, so removing them raises the diameter sharply and breaks the network into isolated clusters error tolerance: because most substrates are sparsely connected, removing random ones leaves the average distance unchanged increasing per-substrate connectivity is what holds the diameter constant as organisms get more complex metabolic network scale-free power-law connectivity diameter reactions ER model number of substrates standard-deviation standard deviation poisson-distribution network-analysis

Method, as described: computational-network-analysis

Legend

second reading	`alternatives`	an independent re-reading of a facet, recorded whether or not it agrees
relation to other work	`claim_relations`	how this paper stands to another: agrees, contradicts, extends, qualifies
claim type	`claim_type`	the shape of the claim: existence, mechanism, method, critique, prediction, null
concept edge	`concept_edges`	an asserted relation between two concepts, with the sentence asserting it
concept	`concepts`	an idea the paper works with, quoted where the paper uses it
content tag	`content_tags`	a finding, definition, quantity, statistic or variable named in the paper
contribution	`contribution`	what the paper claims to add
control	`controls`	an experiment run to eliminate a rival explanation
limitation	`limitations`	what the paper says its evidence cannot support
mechanism	`mechanisms`	how the reported effect is said to come about
method	`method`	how the paper produced its evidence
object of study	`object_of_study`	what the paper is about — the thing it investigates
phenomenon	`phenomenon`	the effect or regularity under study
research question	`research_question`	the question the paper sets itself
sense	`senses`	a distinct use of a term, quoted where the paper fixes it
transfer	`transfers`	a method or concept carried in from another field

The paper

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1038/35036627. The reading view exists for the papers whose licence permits it.

Every tag on this page

alternatives 3 · claim_relations 7 · claim_type 1 · concept_edges 6 · concepts 11 · content_tags 24 · contribution 1 · controls 1 · limitations 5 · mechanisms 4 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 3 · transfers 1

Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; none of 6 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facet	tag	field	conf.	whose words
object_of_study	The core metabolic networks of 43 organisms across archaea, bacteria and eukaryota, as drawn from the WIT pathway-genome database. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`object_of_study`		the paper's words
research_question	Is the topology of a metabolic network the homogeneous random kind predicted by Erdos-Renyi, or the heterogeneous scale-free kind found in the web and in social networks? Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`research_question`		the paper's words
contribution	Shows that metabolic networks in all three domains of life are scale-free, and that their diameter is conserved across organisms of very different complexity - a property the non-biological scale-free networks do not have. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`contribution`		the paper's words
claim_type	existence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_type`		the paper's words
phenomenon	large-scale topology of metabolic networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`phenomenon`		the paper's words
method	network-analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: network-analysis	`method`		the paper's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: growth with preferential attachment: new nodes join by attaching to already well connected ones, which is what produces the power law	`mechanisms[0]`	0.9	the tagger's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hub dominance: a few highly connected substrates carry the connectivity, so removing them raises the diameter sharply and breaks the network into isolated clusters	`mechanisms[1]`	1.0	the tagger's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: error tolerance: because most substrates are sparsely connected, removing random ones leaves the average distance unchanged	`mechanisms[2]`	1.0	the tagger's words
mechanisms	mechanisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: increasing per-substrate connectivity is what holds the diameter constant as organisms get more complex	`mechanisms[3]`	0.9	the tagger's words
limitations	Eighteen of the 43 organisms are not fully sequenced and many ORFs are functionally unassigned, so the substrate and reaction lists analysed are incomplete. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. what this limits: the substrate and reaction lists every topology statistic is computed over: 18 OF THE 43 ORGANISMS ... ARE NOT YET FULLY SEQUENCED, AND A SUBSTANTIAL PORTION OF THE IDENTIFIED ORFs ARE FUNCTIONALLY UNASSIGNED	`limitations[0]`		the tagger's words
limitations	The extension of the conclusion to non-metabolic cellular networks is only preliminary, because those networks are too small for unambiguous statistical analysis with current tools. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. what this limits: the extension beyond metabolism: OUR PRELIMINARY ANALYSIS SUGGEST[s] THAT CONNECTIVITY DISTRIBUTION OF NON-METABOLIC PATHWAYS ALSO FOLLOWS A POWER-LAW - preliminary, and by the authors' own account not statistically decidable	`limitations[1]`		the tagger's words
limitations	18 of the 43 organisms were not fully sequenced and many ORFs are unassigned, so the substrate and reaction lists are known to be incomplete. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. what this limits: the same scope as limitations[0] - the enzyme list is incomplete by construction	`limitations[2]`	1.0	the tagger's words
limitations	The generalisation to other cellular networks is explicitly not supported - those networks are too small for the statistics to be unambiguous. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. what this limits: the same scope as limitations[1], with the reason: THE CURRENT MATHEMATICAL TOOLS DO NOT ALLOW UNAMBIGUOUS STATISTICAL ANALYSIS OF THE TOPOLOGY OF OTHER NETWORKS DUE TO THEIR RELATIVELY SMALL SIZE	`limitations[3]`	1.0	the tagger's words
limitations	The whole analysis rests on one predicted database, whose pathways are inferred from annotated genomes rather than observed. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. what this limits: the object the whole analysis is about: THIS INTEGRATED PATHWAY-GENOME DATABASE PREDICTS THE EXISTENCE OF A GIVEN METABOLIC PATHWAY BASED ON THE ANNOTATED GENOME OF AN ORGANISM, so the network is inferred rather than measured	`limitations[4]`	0.9	the tagger's words
transfers	applying complex-network (scale-free) analysis to the large-scale organization of cellular metabolism Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`transfers[0]`		the tagger's words
controls	the metabolic network topology tested against the inherently random and uniform exponential model as the alternative description Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a scale-free reading of a network that a random model would fit just as well - the paper sets up the exponential model as the thing to rule out before claiming anything else · outcome (stated by the tagger, no quotation): held	`controls[0]`	0.85	the tagger's words
concepts	scale-free network Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: scale-free network	`concepts[0]`		the paper's words
concepts	metabolic network Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: metabolic network	`concepts[1]`		the paper's words
concepts	node Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: node	`concepts[4]`	1.0	the paper's words
concepts	substrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: substrate	`concepts[5]`	1.0	the paper's words
concepts	link Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: link	`concepts[6]`	1.0	the paper's words
concepts	metabolic reactions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: metabolic reactions	`concepts[7]`	1.0	the paper's words
concepts	exponential networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: exponential networks	`concepts[8]`	1.0	the paper's words
concepts	hubs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hubs	`concepts[9]`	1.0	the paper's words
concepts	network diameter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: network diameter	`concepts[10]`	1.0	the paper's words
concepts	biochemical pathway Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: biochemical pathway	`concepts[11]`	1.0	the paper's words
concepts	small-world character Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: small-world character	`concepts[12]`	1.0	the paper's words
senses	network - a metabolic network, where the nodes are chemical substrates and the links are the reactions between them Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[0]`	1.0	the tagger's words
senses	network - the World-Wide Web, the Internet and social networks, cited as the systems where this structure was first reported Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[1]`	1.0	the tagger's words
senses	path - in a metabolic network a path is a biochemical pathway, the chain of reactions from one substrate to another Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`senses[2]`	1.0	the tagger's words
alternatives	claim_type: existence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. a second reading reaching the same value. Recorded: existence — note: a second reading reaching the same value from a different sentence. Not applied - a person decides.	`alternatives.claim_type`		the tagger's words
alternatives	method: comparative Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. a second reading. Recorded: network-analysis — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.	`alternatives.method`		the tagger's words
alternatives	phenomenon: scale-free topology of metabolic networks, with a network diameter conserved across organisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. a second reading. Recorded: large-scale topology of metabolic networks — note: a second reading, verbatim-verified, disagreeing with the value on the record. Not applied - a person decides.	`alternatives.phenomenon`		the tagger's words
claim_relations	builds-on → scale-free network theory Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[0]`		the tagger's words
claim_relations	contradicts → the expectation that network diameter grows with organism complexity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[1]`		the tagger's words
claim_relations	extends → the scale-free / error-tolerant network framework of Barabasi and co-workers (refs 2, 5) Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[2]`		the tagger's words
claim_relations	contradicts → the expectation from previously examined non-biological networks (refs 2, 27, 28) that network diameter grows with the number of nodes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[3]`		the tagger's words
claim_relations	builds-on → barabasi-albert1999-scale-free - growth with preferential attachment Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[4]`	1.0	the tagger's words
claim_relations	extends → the scale-free findings for the World-Wide Web, the Internet and social networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[5]`	1.0	the tagger's words
claim_relations	contradicts → the Erdos-Renyi random network model as a description of cellular networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`claim_relations[6]`	0.7	the tagger's words
concept_edges	node —renamed-across-fields→ substrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 1 also in: node · substrate	`concept_edges[0]`		the tagger's words
concept_edges	link —renamed-across-fields→ metabolic reactions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 1 also in: link · metabolic reactions	`concept_edges[1]`		the tagger's words
concept_edges	metabolic network —is-a→ scale-free network Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 1 also in: metabolic network · scale-free network	`concept_edges[3]`		the tagger's words
concept_edges	scale-free network —contrasted-with→ exponential networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: THE AXIS IS DEGREE HETEROGENEITY. 'Quotation withheld.' Both are networks and both have degree distributions; the contrast is on the SHAPE of that distribution, which is the only property at issue. · strength of the relation: 1 also in: scale-free network · exponential networks	`concept_edges[4]`		the tagger's words
concept_edges	EVIDENCE CORRECTED (RE-GROUNDED) · hubs —part-of→ scale-free network Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. EVIDENCE CORRECTED: RE-GROUNDED. The old span named only one endpoint. This sentence names both and places the hubs inside the network's topology, which is the containment the edge records. — strength of the relation: 1 also in: hubs · scale-free network	`concept_edges[5]`		the tagger's words
concept_edges	hubs —causes→ network diameter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 1 Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span says removing hubs raises the diameter; the edge omits the removal. also in: hubs · network diameter	`concept_edges[6]`		the tagger's words
content_tags	43 — metabolic networks compared, spanning all three domains of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[0]`		the tagger's words
content_tags	P(k) ~ k^-γ — scale-free power-law degree distribution of metabolic networks Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[1]`		the tagger's words
content_tags	43 organisms — size of the comparative sample, spanning all three domains of life Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[2]`	1.0	the tagger's words
content_tags	γin = 2.2 — power-law exponent for incoming links in E. coli Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[3]`	1.0	the tagger's words
content_tags	~4% — share of substrates present in every one of the 43 organisms Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[4]`	1.0	the tagger's words
content_tags	51 substrates — the substrates present in all 43 organisms, used for the rank-order analysis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[5]`	1.0	the tagger's words
content_tags	6 archaea, 32 bacteria, 5 eukaryota — composition of the sample Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.quantities[6]`	1.0	the tagger's words
content_tags	Metabolic networks display the same topologic scaling properties, strikingly similar to the organization of complex non-biological systems. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[0]`		the tagger's words
content_tags	This suggests that metabolic organization is identical for all living organisms and complies with the design principles of robust and error-tolerant scale-free networks. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. about this quote: QUOTE REPAIRED: the extractor split a hyphen-space and the quote was recorded faithfully with the damage in it, which made it unanchorable. The repaired string is an EXACT SUBSTRING of the staged text - that is why it was accepted, not because a rule produced it. The text as originally recorded is kept in evidence as extracted.	`content_tags.findings[1]`		the tagger's words
content_tags	Metabolic networks in all three domains of life are scale-free: the number of reactions a substrate takes part in follows a power law. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[2]`	1.0	the tagger's words
content_tags	Metabolic-network diameter is identical across all 43 organisms, whatever their number of substrates. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[3]`	1.0	the tagger's words
content_tags	The ranking of the most connected substrates is practically identical for all 43 organisms. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[4]`	1.0	the tagger's words
content_tags	Removing randomly chosen substrates, mimicking random mutations, left the average distance between the remaining nodes unaffected: a striking insensitivity to random errors. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.	`content_tags.findings[5]`	1.0	the tagger's words
content_tags	number of substrates Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: number of substrates	`content_tags.variables[2]`	0.9	the tagger's words
content_tags	network diameter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: network diameter	`content_tags.variables[3]`	1.0	the tagger's words
content_tags	hubs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: hubs	`content_tags.definitions[1]`		the tagger's words
content_tags	metabolic network Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: metabolic network	`content_tags.definitions[2]`	1.0	the tagger's words
content_tags	network diameter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: network diameter	`content_tags.definitions[3]`	1.0	the tagger's words
content_tags	ER model Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: ER model	`content_tags.definitions[4]`	1.0	the tagger's words
content_tags	small-world character Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: small-world character	`content_tags.definitions[5]`	1.0	the tagger's words
content_tags	standard-deviation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: standard-deviation	`content_tags.statistics[0]`		the tagger's words
content_tags	power-law Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: power-law	`content_tags.statistics[1]`	1.0	the tagger's words
content_tags	poisson-distribution Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: poisson-distribution	`content_tags.statistics[2]`	1.0	the tagger's words
content_tags	standard-deviation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: standard-deviation	`content_tags.statistics[3]`	1.0	the tagger's words

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