phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | large-scale topology of metabolic networks— “Here we present the first systematic comparative mathematical analysis of the metabolic networks of 43 organisms representing all three domains of life.” | |
| claim-type | existence— “We show that, despite significant variances in their individual constituents and pathways, these metabolic networks display the same topologic scaling properties demonstrating striking similarities to the inherent organization of complex non-biological systems 2.” | |
| method — evidence | — “To begin to address the large-scale structural organization of cellular networks, we have examined the topologic properties of the core metabolic network of 43 different organisms based on data deposited in the WIT database 19.” | |
| object of study — evidence | — “this database provides description for 6 archaea, 32 bacteria and 5 eukaryota” | |
| research question — evidence | — “Our first goal was to identify the structure of the metabolic networks, i.e., to establish if their topology is best described by the inherently random and uniform exponential model 21 (Fig. 1a and b), or the highly heterogeneous scale-free model 2 (Fig. 1c and d).” | |
| contribution — evidence | — “A unique feature of metabolic networks, as opposed to that seen in non-biological scale-free networks, is the apparent conservation of the network diameter in all living organisms.” | |
| transfer | from network science / statistical physics: applying complex-network (scale-free) analysis to the large-scale organization of cellular metabolism— “has benefited from recent advances in understanding the generic properties of complex networks” | transfers[0] |
| mechanism | growth with preferential attachment: new nodes join by attaching to already well connected ones, which is what produces the power law— “the emergence of power law distribution is intimately linked to the growth of the network in which new nodes are preferentially attached to already established nodes 2” | mechanisms[0] |
| mechanism | hub dominance: a few highly connected substrates carry the connectivity, so removing them raises the diameter sharply and breaks the network into isolated clusters— “upon the sequential removal of the mostconnected nodes the diameter of the network rises sharply, the network eventually disintegrating into isolated clusters that are no longer functional” | mechanisms[1] |
| mechanism | error tolerance: because most substrates are sparsely connected, removing random ones leaves the average distance unchanged | mechanisms[2] |
| mechanism | increasing per-substrate connectivity is what holds the diameter constant as organisms get more complex Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | mechanisms[3] |
| builds-on | scale-free network theory Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| contradicts | the expectation that network diameter grows with organism complexity Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| extends | the scale-free / error-tolerant network framework of Barabasi and co-workers (refs 2, 5) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[2] |
| 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[3] |
| builds-on | barabasi-albert1999-scale-free - growth with preferential attachment Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[4] |
| extends | the scale-free findings for the World-Wide Web, the Internet and social networks Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[5] |
| contradicts | the Erdos-Renyi random network model as a description of cellular networks Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[6] |
| sense | network - a metabolic network, where the nodes are chemical substrates and the links are the reactions between them Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[0] |
| sense | network - the World-Wide Web, the Internet and social networks, cited as the systems where this structure was first reported Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[1] |
| sense | path - in a metabolic network a path is a biochemical pathway, the chain of reactions from one substrate to another Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[2] |
| control | the metabolic network topology tested against the inherently random and uniform exponential model as the alternative description — held — rules out 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 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| edge | node —renamed-across-fields→ substrate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| edge | link —renamed-across-fields→ metabolic reactions Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| edge | metabolic network —is-a→ scale-free network Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| differs in | scale-free network —contrasted-with→ exponential networks — THE AXIS IS DEGREE HETEROGENEITY. 'Unlike exponential networks, scale-free networks are extremely heterogeneous, their topology being dominated by a few highly connected nodes (hubs) which link the rest of the less connected nodes to the system.' Both are networks and both have degree distributions; the contrast is on the SHAPE of that distribution, which is the only property at issue. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[4] |
| retracted | EVIDENCE CORRECTED (RE-GROUNDED) · hubs —part-of→ scale-free network — 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. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| audit | hubs —causes→ network diameter — 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. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[6] |
| outcome (stated by the tagger, no quotation) | control — held | controls[0] |
| for which use | limitation — 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 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| for which use | limitation — 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 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| for which use | limitation — the same scope as limitations[0] - the enzyme list is incomplete by construction Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| for which use | limitation — 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 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| for which use | limitation — 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 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| replication | untested | |
| limitation | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| limitation | The generalisation to other cellular networks is explicitly not supported - those networks are too small for the statistics to be unambiguous. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| limitation | The whole analysis rests on one predicted database, whose pathways are inferred from annotated genomes rather than observed. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Metabolic networks display the same topologic scaling properties, strikingly similar to the organization of complex non-biological systems. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| evidence status note | finding — 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] |
| finding | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| finding | Metabolic-network diameter is identical across all 43 organisms, whatever their number of substrates. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[3] |
| finding | The ranking of the most connected substrates is practically identical for all 43 organisms. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[4] |
| finding | 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 paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[5] |
| quantity | 43 organisms — metabolic networks compared, spanning all three domains of life Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| quantity | P(k) ~ k^-γ — scale-free power-law degree distribution of metabolic networks Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[1] |
| quantity | 43 organisms — size of the comparative sample, spanning all three domains of life Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[2] |
| quantity | γin = 2.2 — power-law exponent for incoming links in E. coli Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[3] |
| quantity | ~4% — share of substrates present in every one of the 43 organisms Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[4] |
| quantity | 51 substrates — the substrates present in all 43 organisms, used for the rank-order analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[5] |
| quantity | 6 archaea, 32 bacteria, 5 eukaryota — composition of the sample Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[6] |
| variable | number of substrates (independent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[2] |
| variable | network diameter (dependent) Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[3] |
| definition | hubs Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| definition | metabolic network Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[2] |
| definition | network diameter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[3] |
| definition | ER model Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[4] |
| definition | small-world character Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[5] |
| key-terms | metabolic, network, substrate, scale-free, power-law, connectivity, diameter, hubs, reactions, metabolic network, node, link, scale-free network, network diameter, small-world character, biochemical pathway, exponential networks, metabolic reactions |
| concept | scale-free network Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[0] |
| concept | metabolic network Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[1] |
| concept | node — not defined in this paper's own words; an element of the network; here, a chemical substrate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[4] |
| concept | substrate — not defined in this paper's own words; a chemical compound consumed or produced by a metabolic reaction; what a node is in this field Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[5] |
| concept | link — not defined in this paper's own words; a connection between two nodes; here, a metabolic reaction, and directed because reactions are catalysed one way Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[6] |
| concept | metabolic reactions — not defined in this paper's own words; the biochemical conversion that joins two substrates; what an edge is in this field Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[7] |
| concept | exponential networks — not defined in this paper's own words; a homogeneous network in which the chance of a highly connected node falls off exponentially, so hubs are effectively absent Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| concept | hubs — not defined in this paper's own words; the few nodes carrying most of the connections, on which the network's diameter depends Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[9] |
| concept | network diameter — not defined in this paper's own words; the shortest path between two substrates, averaged over every pair - the paper's measure of interconnectivity Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[10] |
| concept | biochemical pathway — not defined in this paper's own words; a chain of reactions linking one substrate to another; what a path through the graph is in this field Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[11] |
| concept | small-world character — not defined in this paper's own words; the property that any two nodes are joined by a relatively short path Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[12] |
| standard-deviation SD/σ | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[0] |
| power-law P(k) ~ k^-γ | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[1] |
| poisson-distribution Poisson | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[2] |
| standard-deviation σ | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[3] |
| claim type | existence — a second reading reaching the same value; recorded: existence Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.claim_type |
| method | comparative — a second reading; recorded: network-analysis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.method |
| phenomenon | scale-free topology of metabolic networks, with a network diameter conserved across organisms — a second reading; recorded: large-scale topology of metabolic networks Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | alternatives.phenomenon |
When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.
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