papers/paperspec
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
c7f54320dd56d019de8cc6ad8ff60e0aa64e5bda
paperspec/fixtures/records/layer/annotations.jsonl
T
alexmandClaude c7f54320dd refactor!: claim references are claim:TAG 
lode is renamed paperclaim. A claim reference is claim:TAG or
claim:host/TAG and a pin claim:TAG@hex6 (claimRef and claimPin in
common.schema.json, spec/18 §18.4, spec/02, spec/20); the eight-character
tags do not change. A project names its claim namespace as
claims.paperclaim, and the main example's targeted receipts take the
scope targeted:paperclaim. No old prefix or name is accepted.

paperspec build regenerated the fixtures and vectors: the claim link's and
the symbol's record IDs, the layer receipt, project.json, the two targeted
receipts and Ben's spot-check, the QA report, the inclusion proof, the log's
checkpoint and tiles, and the signature, spot-check, VRF and checkpoint
vectors. The walkthrough and examples quote the new receipt IDs.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SarHTuHhV9cS85XWy2NrLJ
2026-10-17 10:38:53 -04:00

13 lines
15 KiB
JSON
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"audience":"novice","format":"text/markdown","kind":"gloss","language":"en","type":"TextualBody","value":"A *harmonic* term treats a bond like a spring: the energy grows with the square of the stretch."},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/f4s8pc1hdhd9d","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"describing","receipt":"w9j3dwgydy2e0","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"rr20tev","node_hash":"76e06b4811a688357ac4b912172283463cfaf1b7a1f0795d274fc733a2309ba7","own_hash":"2d7df7b8b233eab6f96d5db0d29c99062aaa94b55cf4e388c49b9995ce7548d5","quote":{"exact":"bond force constant","prefix":"rm{eq}})^2$$ where $K_r$ is the ","suffix":" and $r_\\mathrm{eq}$ the equilib"},"rev":12,"span":[111,130],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"bond force constant","prefix":"rm{eq}})^2$$ where $K_r$ is the ","suffix":" and $r_\\mathrm{eq}$ the equilib","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"claim-link","pin":"claim:272XTX7C@02f47b","role":"states","source":"claim:272XTX7C","type":"SpecificResource"},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/m2vbd164hfkc3","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"linking","receipt":"w9j3dwgydy2e0","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"rr20tev","node_hash":"76e06b4811a688357ac4b912172283463cfaf1b7a1f0795d274fc733a2309ba7","own_hash":"2d7df7b8b233eab6f96d5db0d29c99062aaa94b55cf4e388c49b9995ce7548d5","quote":{"exact":"The bond energy is given by $$E_{\\mathrm{bond}} = \\frac{1}{2} K_r (r - r_{\\mathrm{eq}})^2$$ where $K_r$ is the bond force constant and $r_\\mathrm{eq}$ the equilibrium bond length."},"rev":12,"store":"smithlab"},"type":"AnchorSelector"},{"exact":"The bond energy is given by $$E_{\\mathrm{bond}} = \\frac{1}{2} K_r (r - r_{\\mathrm{eq}})^2$$ where $K_r$ is the bond force constant and $r_\\mathrm{eq}$ the equilibrium bond length.","prefix":"","suffix":"","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"category":"critique","kind":"comment","type":"TextualBody","value":"The step size matters more than the text admits."},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/sxj4eq8415s92","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"commenting","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"xjns57z","node_hash":"42b1de7852cdc68730984fff789fe248ecd5b43198c0e7d671931ff3fe561dc3","own_hash":"4dc28d1ad57c74d044f87264dfbc744ae9d5e9644638db976dbc346361442486","quote":{"exact":"steps of 0.01","prefix":"Each bond was scanned in ","suffix":" Å around its minimum, and the e"},"rev":12,"span":[25,38],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"steps of 0.01","prefix":"Each bond was scanned in ","suffix":" Å around its minimum, and the e","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"category":"question","for":"group","kind":"question","type":"TextualBody","value":"Why fit to a scan first and to frequencies second?"},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/fsg960szdyy6q","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"questioning","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"section","node":"d400rz3","node_hash":"e5a8eeb3c112f2dc3341da8f433540a3fc5a7e7f631e72c4dd36c6933aae808d","own_hash":"c3d50f266b05d7889c001aef16662cecd4e99ac4a2747ec331c1044e6adc8e3e","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"citation-context","reason":"value","reference":"vxsdvzq","type":"TextualBody","value":"Cited for the band position; the reference is not in the library.","verdict":"cannot-tell"},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/gbj7nn87ndfd8","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"assessing","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"hca6dc5","node_hash":"8cfed5a34aab28517e89e8a164f0f96c14361de83ebc800439116e83ef479f34","own_hash":"c270571517825ceed31ca912b80ac76203effe47f1c84f8ee8962800d0afc92f","quote":{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2"},"rev":12,"span":[71,75],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"generator":{"model":{"name":"example-model","parameters":"998b5161e39e01c8bc43ef81ec89141e15b7ea53b2e936707920a6097dbcb2c5","processor":"local","prompt":"9cc338fba7c62db7266f530cb555a5ee36910d41a0120a3fe7fd7de1944d0931","provider":"Example Models (illustrative)","version":"2026-09","weights":"504b2d340045b92c22682b60020c21103aae7ff41172bb632fbe305eb4af9b5e"},"run":"illustrative-run-1"},"kind":"generated","type":"TextualBody","value":"Two panels: an energy scan and its fit residual."},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:software:example-model","name":"A model (illustrative)","type":"Software"},"id":"tag:scient.ing,2026:annotation:smithlab/szb6k3fj9z7aw","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"describing","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"figure","node":"v7cx6qs","node_hash":"f76864779843485fa9e2f3cc3cd1c76ad222e1649c56f4cface33bf20b8f33b6","own_hash":"a1e46cb40201a17903dfd6f128db1e707b0e9f5bf45fcc32ec7ca772011edeae","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"exercise":{"exercise":"anchor","format":"scienting-exercise/1","key":{"elements":[{"anchors":[{"context":{"column_path":["Set A","$K_r$ (kcal mol⁻¹ Å⁻²)"],"row_path":["Bond parameters","CT–CT"],"table_label":"Table 1"},"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"cell","node":"c20cna6","node_hash":"c8e6a553f5ae1377776e86dde6ee7d48a923dea7de417408841ea33b81563272","own_hash":"45bf6ab427d435f28b82cb2b64d93c502968921507fc9397abd5d5170731c6ab","quote":{"exact":"310.0"},"rev":12,"store":"smithlab"}],"feedback":{"hit":"That is the cell.","miss":"Look in Table 1, row CT–CT."},"points":"1"}]},"prompt":"Find the table cell that gives the Set A bond constant for the CT–CT bond.","rule":{"match":"same-node"}},"kind":"exercise","type":"TextualBody","value":"Find the table cell that gives the Set A bond constant for the CT–CT bond."},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/whcypxav2cqbx","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"assessing","receipt":"w9j3dwgydy2e0","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"table","node":"hj4s7pb","node_hash":"6c6fba200faf41cd06fa8b64e06e2aa29ff8848568b859ae42d1902596348643","own_hash":"66310a9ab1c92568f4c6cae012e35d4245d4ca4b89d2542b7c2113a31ad379ed","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"exercise":{"exercise":"check","format":"scienting-exercise/1","key":{"elements":[{"anchors":[{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"kea5026","node_hash":"b836d5872ca37471fa996be04c538254a8b1e37ca12e8f1b4a40837b503afa33","own_hash":"d673d236c03d9583ecf6e01fa819765ec324dc684bd9bbc6967fa50f216e34d2","quote":{"exact":"the most common description","prefix":"Harmonic bond terms remain ","suffix":" of covalent stretching in class"},"rev":12,"span":[27,54],"store":"smithlab"}],"points":"1"}],"verdict":{"points":"1","value":"supports"}},"prompt":"Does the cited passage support the claim that harmonic terms are the most common choice?","rule":{"match":"overlap","min_overlap":"0.5"}},"kind":"exercise","type":"TextualBody","value":"Does the cited passage support the claim that harmonic terms are the most common choice?"},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/y7bd3he0jwjbx","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"assessing","receipt":"w9j3dwgydy2e0","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"kea5026","node_hash":"b836d5872ca37471fa996be04c538254a8b1e37ca12e8f1b4a40837b503afa33","own_hash":"d673d236c03d9583ecf6e01fa819765ec324dc684bd9bbc6967fa50f216e34d2","quote":{"exact":"Harmonic bond terms remain the most common description of covalent stretching in classical force fields.1"},"rev":12,"store":"smithlab"},"type":"AnchorSelector"},{"exact":"Harmonic bond terms remain the most common description of covalent stretching in classical force fields.1","prefix":"","suffix":"","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"description","language":"en","role":"alt","type":"TextualBody","value":"Energy along the C–C bond stretch (panel a) and the fit residual (panel b)."},"created":"2026-10-11T19:00:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/gb5tmv3hq08vz","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"describing","receipt":"w9j3dwgydy2e0","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"figure","node":"v7cx6qs","node_hash":"f76864779843485fa9e2f3cc3cd1c76ad222e1649c56f4cface33bf20b8f33b6","own_hash":"a1e46cb40201a17903dfd6f128db1e707b0e9f5bf45fcc32ec7ca772011edeae","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"category":"comment","kind":"comment","type":"TextualBody","value":"Agreed; see the residual panel."},"created":"2026-10-11T19:05:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/t5cv4rec7j0mt","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"replying","status":"proposed","target":{"source":"tag:scient.ing,2026:annotation:smithlab/sxj4eq8415s92","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"category":"context","kind":"caveat","type":"TextualBody","value":"The band position is cited, not measured here; reference 2 is not in the library."},"created":"2026-10-11T19:10:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/g7ngzk3jkdy40","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"commenting","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"hca6dc5","node_hash":"8cfed5a34aab28517e89e8a164f0f96c14361de83ebc800439116e83ef479f34","own_hash":"c270571517825ceed31ca912b80ac76203effe47f1c84f8ee8962800d0afc92f","quote":{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2"},"rev":12,"span":[71,75],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"key":"K_{r}","kind":"symbol","pin":"claim:272XTX7C@02f47b","source":"claim:272XTX7C","symbol":"K_r","type":"SpecificResource"},"created":"2026-10-11T19:15:00Z","creator":{"id":"tag:scient.ing,2026:key:ana","name":"Ana Example","type":"Person"},"id":"tag:scient.ing,2026:annotation:smithlab/f2603vdj2e3tr","layer":"tag:scient.ing,2026:layer:smithlab/kp4m2x7q","motivation":"identifying","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic-damb","format":"scienting-anchor/1","kind":"sentence","node":"rr20tev","node_hash":"76e06b4811a688357ac4b912172283463cfaf1b7a1f0795d274fc733a2309ba7","own_hash":"2d7df7b8b233eab6f96d5db0d29c99062aaa94b55cf4e388c49b9995ce7548d5","quote":{"exact":"$K_r$","prefix":"(r - r_{\\mathrm{eq}})^2$$ where ","suffix":" is the bond force constant and "},"rev":12,"span":[98,103],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"$K_r$","prefix":"(r - r_{\\mathrm{eq}})^2$$ where ","suffix":" is the bond force constant and ","type":"TextQuoteSelector"}],"source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb","type":"SpecificResource"},"type":"Annotation"}
Reference in new issue View Git Blame Copy Permalink