Reference & citation management
Collect references, fix metadata and insert a correctly formatted bibliography.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- Zotero · EndNote · Mendeley
- Class GUI-need label
HY· Hybrid
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R04.06.01.02-T01 Add twelve papers by DOI into a new Zotero collection
Original instruction
In Zotero (test profile), create collection 'Thesis Ch2' and add the 12 works whose DOIs are in input/ch2_dois.txt using Add Item by Identifier (sandbox resolver), so each item has full metadata and appears only in that collection. Do not add duplicates of the 3 already in the library; add those to the collection instead.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
zotero.sqlite (read after closing Zotero): collection with 12 items whose DOI fields equal the list; no duplicate DOIs in library; titles/authors/years equal resolver key; 3 pre-existing item ids reused.
Proposed partial credit
15% collection; 50% items added with metadata; 25% no duplicates; 10% membership correct.
R04.06.01.02-T02 Correct item types and missing fields for eight Zotero records
Original instruction
In Zotero collection 'To fix', 8 items have wrong item types (a conference paper stored as journal article, a thesis as book) or missing fields (journal abbreviation, pages, volume, issue). Correct them per input/metadata_key.csv without creating new items.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
zotero.sqlite: same 8 itemIDs; itemType and field values equal CSV; attachments and notes still linked; no new items.
Proposed partial credit
40% item types; 50% fields (pro-rata); 10% ids/attachments preserved.
R04.06.01.02-T03 Insert ten live Zotero citations and an APA bibliography in Word
Original instruction
In input/manuscript.docx, 10 places are marked '[CITE: doi]'. Replace each marker with a live Zotero citation (Zotero Word plugin) to the matching library item, style APA 7th, combine adjacent markers into one parenthetical citation, and insert the bibliography under 'References'.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickmulti· Cross-app- Work product
WP01· Document- Conditions
multiapp· Multi-app- Proposed difficulty
- 3 / 5
Proposed verifier
docx fields: ADDIN ZOTERO_ITEM CSL_CITATION JSON at each marker position with the right item URIs; markers gone; one ZOTERO_BIBL field; document prefs style apa; rendered citation text equals CSL processor output.
Proposed partial credit
50% citations linked (pro-rata); 15% adjacency combined; 25% bibliography; 10% style.
R04.06.01.02-T04 Cite while you write in Vancouver style with EndNote
Original instruction
Using EndNote with Word, insert numbered Vancouver citations for the 14 references marked '{Author, Year}' in input/review_draft.docx from library input/review.enl, so numbers follow order of first citation, ranges collapse (3–5), and the reference list appears at the end.
- Platforms
mac· macOSwin· Windows- Applications
- EndNote · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickmulti· Cross-app- Work product
WP01· Document- Conditions
licensed· Licensed pro appmultiapp· Multi-app- Proposed difficulty
- 3 / 5
Proposed verifier
docx: ADDIN EN.CITE fields at each marker with record numbers from review.enl; numbering order by first appearance; collapsed ranges where consecutive; ADDIN EN.REFLIST with 14 entries in Vancouver format.
Proposed partial credit
45% citations linked; 25% numbering/ranges; 30% reference list.
R04.06.01.02-T05 Merge fifteen duplicate pairs in a Zotero library without losing data
Original instruction
The Zotero library has 15 duplicate pairs (Duplicate Items pane). Merge each pair keeping as master the version that has the PDF attachment, and make sure tags, notes and collection memberships of both versions survive on the merged item.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & click- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
zotero.sqlite: 15 fewer items; survivors are the PDF-holding itemIDs; merged items carry the union of tags, child notes and collections; deleted duplicates in trash with relations 'dc:replaces'.
Proposed partial credit
35% pairs merged; 25% correct master; 30% tags/notes/collections union; 10% replaces relations.
R04.06.01.02-T06 Organize a Mendeley library into collections and attach PDFs
Original instruction
In Mendeley Reference Manager (test account), sort the 40 references in 'Unsorted' into collections 'Methods', 'Background', 'Datasets' per input/mendeley_map.csv, attach the PDFs in input/pdfs/ to their references by matching title, and star the 5 listed as key papers.
- Platforms
mac· macOSwin· Windows- Applications
- Mendeley
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & click- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Mendeley API (grader read-only token): folder memberships equal CSV; file attachments with hashes matching the right documents; starred flag on 5; no duplicates created.
Proposed partial credit
40% collections; 40% PDFs attached correctly; 10% stars; 10% no duplicates.
R04.06.01.02-T07 Switch a manuscript's citation style and add page locators
Original instruction
input/chapter3.docx has live Zotero citations in APA. Switch the document to Chicago Manual of Style 17th (author-date), add page locators to the 6 citations listed in input/locators.csv, suppress the author in the 2 narrative citations marked, and refresh the bibliography.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP01· Document- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Document prefs style id chicago-author-date; the 6 citation JSONs carry locator/label 'page' with values equal CSV; 2 with suppress-author true; rendered text equals CSL output; bibliography refreshed.
Proposed partial credit
25% style switched; 40% locators; 20% suppress author; 15% refresh.
R04.06.01.02-T08 Clean a BibTeX library in JabRef so the paper compiles warning-free
Original instruction
Open input/refs.bib (85 entries) in JabRef: regenerate citation keys with pattern [auth][year][shorttitle:lower], fix the 10 entries flagged by input/biber_warnings.log (missing fields, bad dates), and save. Update input/paper.tex \cite keys to the new keys so it compiles with biber with 0 warnings.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- JabRef · TeX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
bib parse: keys follow the pattern and are unique; flagged fields fixed per key; latexmk + biber run: 0 warnings, 0 undefined citations; every \cite resolves to the same work as before (DOI mapping).
Proposed partial credit
30% keys regenerated; 30% flagged fixes; 25% clean compile; 15% cites mapped correctly.
R04.06.01.02-T09 Build a Zotero saved search for items still missing PDFs
Original instruction
In Zotero create saved search 'Needs PDF' matching items in collection 'Thesis' (incl. subcollections) added in 2025 or later, of type journal article or conference paper, with no PDF attachment. Tag every current match 'todo-pdf'.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
zotero.sqlite savedSearchConditions equal spec (collection recursive, dateAdded, itemType OR, attachment file type); grader evaluates the search: result set equals key (17 items); tag 'todo-pdf' on exactly those.
Proposed partial credit
50% saved search conditions; 30% correct result set; 20% tags.
R04.06.01.02-T10 Turn 34 plain-text citations into live Zotero citations
Original instruction
input/thesis_ch4.docx has 34 plain-text author-date citations like '(Nguyen et al., 2019a)'. Replace each with a live Zotero citation to the right item in the library (resolve 2019a/2019b by the reference list at the end), keep page numbers as locators, then replace the static reference list with a Zotero bibliography.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & formsnav· Pan/zoom/scroll- Work product
WP01· Document- Conditions
multiapp· Multi-app- Proposed difficulty
- 4 / 5
Proposed verifier
34 ZOTERO_ITEM fields at the original positions with item URIs equal key (incl. a/b disambiguation); locators preserved; no plain-text citations remain (regex); static list removed and ZOTERO_BIBL present.
Proposed partial credit
55% citations correctly linked (pro-rata); 15% a/b disambiguation; 10% locators; 20% bibliography swap.
R04.06.01.02-T11 Import, de-duplicate and format a systematic-review library in EndNote
Original instruction
In EndNote create output/sr_library.enl, import input/pubmed.nbib, input/embase.ris and input/scopus.ris, de-duplicate (DOI, then title+year), put survivors in group set 'Screening' groups by source, and modify a copy of the Vancouver style so 'et al.' follows 3 authors; export the bibliography as output/included.rtf.
- Platforms
mac· macOSwin· Windows- Applications
- EndNote
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
licensed· Licensed pro app- Proposed difficulty
- 4 / 5
Proposed verifier
Library DB: record count equals unique key (412); no DOI duplicates; groups per source; modified style file with author-list abbreviation 3; RTF bibliography entries equal formatted key for 20 sampled records.
Proposed partial credit
25% imports; 30% de-dup count; 15% groups; 30% style + export.
R04.06.01.02-T12 Adapt a CSL style to a journal's rules and apply it
Original instruction
The journal in input/author_guidelines.pdf wants APA-like references but with DOIs as 'https://doi.org/…', sentence-case article titles, and journal names abbreviated. Create a modified CSL style 'Journal X' (Zotero style editor), install it in Zotero, and apply it to input/submission.docx.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
code· Code & commandsclick· Point & click- Work product
WP01· Document- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Installed style XML validates against CSL 1.0.2 schema; rendering 15 test items with citeproc equals expected strings; document prefs reference the new style id; bibliography text equals expected output.
Proposed partial credit
40% style rules correct on test items; 15% valid CSL; 20% installed; 25% applied to document.
R04.06.01.02-T13 Cite with Zotero in Google Docs and switch the document to IEEE
Original instruction
In Google Doc 'Policy brief draft' (test account), use the Zotero connector to insert citations for the 8 items marked '[cite: title]' from the Zotero group 'Policy Lab', add the bibliography at the end, then switch the document style to IEEE so citations become numbered.
- Platforms
web· Any OS (web)- Applications
- Zotero · Google Docs
- Interfaces
brow· Browser- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickmulti· Cross-app- Work product
WP01· Document- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Docs API read: markers gone; Zotero citation links (zotero.org/google-docs/?… named ranges) at 8 positions with item keys equal key; numbered [n] text in IEEE order; bibliography present with 8 entries.
Proposed partial credit
50% citations linked; 25% IEEE numbering; 25% bibliography.
R04.06.01.02-T14 Merge two co-authors' cited manuscripts onto a shared group library
Original instruction
input/part_a.docx and input/part_b.docx cite the same works from two personal Zotero libraries. Combine them into output/joint_paper.docx whose citations all point to the matching items in Zotero group 'Joint Project' (use Unlinked Citations / relinking), with one unified bibliography and no duplicate entries.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickmulti· Cross-appnav· Pan/zoom/scroll- Work product
WP01· Document- Conditions
long· Long-horizonmultiapp· Multi-app- Proposed difficulty
- 5 / 5
Proposed verifier
Every ZOTERO_ITEM URI points to group 'Joint Project' items (by group id) matched via DOI/title; no URIs to personal libraries; bibliography entry count equals unique works (47); text of both parts present in order.
Proposed partial credit
50% citations relinked to group items; 20% no duplicates; 20% bibliography; 10% content merged.
R04.06.01.02-T15 Migrate a 400-reference EndNote library and its manuscript to Zotero
Original instruction
Move input/lab.enl (400 refs, PDFs, notes, 12 groups) into Zotero with groups as collections and PDFs as stored attachments, then convert input/grant_draft.docx's EndNote citations to live Zotero citations to the migrated items so the bibliography regenerates identically in the same style.
- Platforms
mac· macOSwin· Windows- Applications
- EndNote · Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
HY· Hybrid- Interaction primitives
click· Point & clickmulti· Cross-appnav· Pan/zoom/scroll- Work product
WP02· Records/table- Conditions
licensed· Licensed pro applong· Long-horizonmultiapp· Multi-app- Proposed difficulty
- 5 / 5
Proposed verifier
zotero.sqlite: 400 items with 12 collections matching groups; attachment hashes equal; notes count equal; docx has no EN.CITE fields, ZOTERO_ITEM fields reference migrated items; regenerated bibliography text equals original (normalized).
Proposed partial credit
30% items/metadata; 20% collections; 15% attachments; 35% manuscript citations converted.
R04.06.01.02-T16 Extract Zotero PDF annotations into an evidence matrix workbook
Original instruction
For the 30 papers in Zotero collection 'Review', extract annotations to notes, then build output/evidence_matrix.xlsx with one row per paper: citekey, design, sample size, primary outcome, effect size (from highlights colored yellow = outcome, green = design, blue = sample), and a live Zotero link (zotero://select) per row.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Excel
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
HY· Hybrid- Interaction primitives
click· Point & clickmulti· Cross-apptype· Text & forms- Work product
WP02· Records/table- Conditions
long· Long-horizonmultiapp· Multi-app- Proposed difficulty
- 5 / 5
Proposed verifier
zotero.sqlite: 30 child notes generated from annotations; workbook rows equal key fields (exact for sample size/effect size, normalized for text); links resolve to correct item keys.
Proposed partial credit
20% annotation notes; 60% matrix fields (pro-rata); 20% links.
R04.06.01.02-T17 Control pair of T08: regenerate BibTeX keys and fix fields by script
Original instruction
Control pair of T08. From the terminal, use a Python BibTeX library (bibtexparser) to regenerate keys with the same pattern, fix the 10 flagged entries, update \cite keys in input/paper.tex, and compile with latexmk/biber with 0 warnings.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- bibtexparser · TeX
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Same checker as T08; compared against the JabRef variant.
Proposed partial credit
30% keys; 30% fixes; 25% compile; 15% mapping.
R04.06.01.02-T18 Color-code highlights in Zotero's PDF reader by evidence type
Original instruction
In Zotero's built-in reader, annotate 5 PDFs in collection 'Pilot': highlight each paper's primary outcome sentence yellow, study design sentence green and sample-size sentence blue (exact sentences listed by page in input/targets.csv), and add a comment 'RoB: low/high' to the design highlight per the CSV.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clicktype· Text & forms- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
zotero.sqlite itemAnnotations: 15 highlights with colors per type; position rects cover target sentence tokens (token F1 ≥0.95); comments on design highlights equal CSV; no extra annotations. Agent has no Zotero web API key, Zotero's Run JavaScript tool and local connector API are disabled, and zotero.sqlite is locked while Zotero runs.
Proposed partial credit
60% highlights exact (pro-rata over 15); 20% colors; 20% comments.
R04.06.01.02-T19 Replace citations of retracted papers flagged by Zotero
Original instruction
Zotero flags 3 retracted items cited in input/review_v2.docx. Tag them 'retracted', move them to collection 'Retracted', and in the manuscript replace each of their citations with the replacement works in input/replacements.csv (already in the library), then refresh the bibliography so retracted items vanish.
- Platforms
mac· macOSwin· Windows- Applications
- Zotero · Word
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clickmulti· Cross-app- Work product
WP01· Document- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
zotero.sqlite: tags and collection membership on 3 retracted items; docx: no ZOTERO_ITEM references to them; replacement items cited at the same positions; bibliography excludes retracted entries.
Proposed partial credit
20% tagged; 15% collection; 45% citations replaced; 20% bibliography updated.
R04.06.01.02-T20 Set up a pinned-key Better BibTeX auto-export for an Overleaf paper
Original instruction
In Zotero with Better BibTeX, pin citation keys for collection 'Paper 2026' to the keys used in input/paper.tex (some items currently get different keys), set up an auto-export of that collection to output/paper.bib (BibLaTeX, on change), and confirm paper.tex compiles with all citations resolved.
- Platforms
mac· macOSwin· Windowslin· Linux- Applications
- Zotero · TeX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
Better BibTeX DB: pinned keys (Citation Key field) equal \cite keys for all items; auto-export job for the collection to output/paper.bib with on-change; grader edits an item title and confirms the .bib updates; latexmk shows 0 undefined citations.
Proposed partial credit
40% keys pinned; 25% auto-export configured; 15% updates on change; 20% clean compile.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.