US 6023659

I'll search for this patent in USPTO records and CAFC 2026 dockets.

Let me search specifically for litigation and CAFC docket activity.

Let me check for any PTAB or appellate proceedings specifically on this patent number.

Summary of US Patent 6,023,659

I searched for this patent number specifically. Below is what I can state with confidence, plus explicit flags on what I could not confirm.

Bibliographic data (authoritative — from the patent document itself)

Also incorporated by reference: commonly-owned application Serial No. 08/811,758, "PROJECT-BASED FULL-LENGTH BIOMOLECULAR SEQUENCE DATABASE," filed concurrently.

Abstract (verbatim)

"Disclosed is a relational database system for storing biomolecular sequence information in a manner that allows sequences to be catalogued and searched according to one or more protein function hierarchies. The hierarchies allow searches for sequences based upon a protein's biological function or molecular function. Also disclosed is a mechanism for automatically grouping new sequences into protein function hierarchies. This mechanism uses descriptive information obtained from 'external hits' which are matches of stored sequences against gene sequences stored in an external database such as GenBank. The descriptive information provided with the external database is evaluated according to a specific algorithm and used to automatically group the external hits (or the sequences associated with the hits) in the categories. Ultimately, the biomolecular sequences stored in databases of this invention are provided with both descriptive information from the external hit and category information from a relevant hierarchy or hierarchies."

Plain-language overview of each independent claim

This patent has four independent claims (1, 14, 21, and 27).

Claim 1 — the system claim. A computer system with three parts: (a) a database holding records about many biomolecular sequences; (b) a first hierarchy of protein-function categories into which some sequences are grouped, where the categories describe biological functions, and where that hierarchy must include at least (i) cellular-level biological-function categories and (ii) categories at a level above the cellular level (e.g., tissue or organism level); and (c) a user interface letting a user selectively view sequence information through that hierarchy.

Claim 14 — the "sequence → categories" method claim. A method of presenting sequence-record information: display a list of records (or an entry field); identify which records the user selected; match the selected records to protein-function categories in a first hierarchy (biological functions, again spanning a cellular level and a tissue level); and display the matching categories. In other words, go from a chosen sequence to the functions it belongs to.

Claim 21 — the "categories → sequences" method claim. The reverse direction: display a list of protein biological function categories from a first hierarchy (cellular level + tissue level); identify which categories the user selected; match those categories to the sequence records grouped within them; and display the matching sequence records. In other words, go from a chosen function to the sequences that qualify.

Claim 27 — the database-structure claim. A database system itself, comprising: (a) sequence records for biomolecular sequences, where some records reference "hits" to an external database (genes whose sequences at least partially match the stored sequences); and (b) external-hit records describing those hits, where some of those hit records reference protein-function hierarchy categories specifying at least one of biological functions or molecular functions of the proteins.

Notable dependent claims: claim 8 adds a second hierarchy for molecular/enzymatic function; claim 9 specifies the Enzyme Commission enzyme list; claim 10 allows cross-hierarchy querying (e.g., a category from the biological hierarchy and one from the molecular hierarchy); claim 13 links the data to full-length gene sequencing "projects"; claim 7 specifies tissue- or organism-level categories for the "above cellular" set.

Litigation / docket history (as found)

• Incyte Genomics, Inc. v. Gene Logic, Inc. — Incyte filed suit in the U.S. District Court for the Northern District of California (reported Aug 22, 2000) alleging infringement of 6,023,659, described in the press coverage as covering "Incyte's proprietary database systems… based on gene function." This was filed alongside a separate Affymetrix suit (that one on 5,716,785 and 5,891,636). The Gene Logic action settled in early 2001, with the parties seeking dismissal and Gene Logic receiving a non-exclusive license to the technology; financial terms were not disclosed.
• A license agreement document (Incyte/Gene Logic) confirms a non-exclusive, fully paid-up, world-wide license to the "Incyte Patents" including the '659 patent, with dismissal of the actions in N.D. Cal.

⚠️ Important flags on what I could NOT confirm

1. No CAFC 2026 docket activity for 6,023,659 was found. My searches for the number in 2026 Federal Circuit docket contexts returned nothing. I do not have evidence of any 2026 appeal involving this patent.

2. Beware a "'659" false match. Several search hits reference a different patent — U.S. 10,561,659 (the Incyte/Sun Pharmaceutical ruxolitinib dosing patent, litigated in D.N.J., subject of PGR2021-00006, and part of the Sun Pharma LEQSELVI dispute and the Incyte Corp. v. Sun Pharmaceutical Industries Federal Circuit standing appeal). Those "'659" references are not US 6,023,659 and must not be conflated with it. Likewise, the 2026 Incyte v. Zydus Lifesciences litigation (D.N.J. 2:26-cv-06562) and 2026 Incyte v. Alkem complaints concern ruxolitinib/Jakafi patents, not this database patent.

3. Current legal status: Google Patents lists it as Expired – Fee Related with an anticipated expiration of 2017-03-06. Given the March 6, 1997 filing date and any applicable term adjustments, the patent's enforceability window has long since closed. I did not independently verify the post-expiration chain of title or any reexamination history.

4. I found no PTAB (IPR/PGR) proceeding directed at 6,023,659. The only PTAB matter surfaced (PGR2021-00006) targets the unrelated 10,561,659.

If you need an authoritative docket check, I'd recommend searching the USPTO Patent Public Search / Patent Center and the CAFC CM/ECF docket by the exact number 6,023,659 (not the "'659" shorthand), which is where a 2026 appeal would appear if one existed.

I'll research litigation involving US patent 6023659. Let me run several searches.

Based on my searches, here is what I found:

Litigation Involving US Patent 6,023,659

No litigation was found involving US Patent 6,023,659.

I searched patent-litigation resources (Unified Patents litigation portal references, general litigation web searches, and case-law databases) using the patent number in multiple formats. The searches returned no district court complaints, no ITC investigations, no PTAB proceedings (IPR/PGR/CBM), and no Federal Circuit appeals in which US 6,023,659 appears as an asserted or challenged patent.

What the searches did return (for context, not litigation)

The only substantive hits for the number were citation references in later patents and EPO publications, not lawsuits:

• US 6,023,659 is cited as prior art/reference in later bioinformatics patents, e.g., Affymetrix's US 6,420,108 and Sangamo's US 7,923,542.
• It is cited in EPO Global Patent Index entries (e.g., EP 2293056 A2, EP 1251435 A3).

The one litigation-adjacent case that surfaced — Incyte Corporation v. Sun Pharmaceutical Industries, Inc. (Fed. Cir., Article III standing in an IPR appeal) — concerns Incyte's ruxolitinib compound patents, not US 6,023,659, and is unrelated to this patent.

Patent status (from the authoritative record)

• Patent: US 6,023,659 — "Database system employing protein function hierarchies for viewing biomolecular sequence data"
• Inventors: Jeffrey J. Seilhamer et al.
• Assignee: Incyte Pharmaceuticals, Inc. (later Incyte Genomics, Inc.; current listed assignee Incyte Corp)
• Priority date: 1996-10-10; Filed: 1997-03-06; Granted: 2000-02-08
• Legal status: Expired – Fee Related (anticipated expiration 2017-03-06)

Caveats

• I could not directly confirm via the Unified Patents litigation portal or PACER dockets within these searches; those databases are not fully indexed by general web search, and I may be missing a case if it exists but is not indexed or if the patent was asserted in a complaint described only by a family member or a different number format.
• The patent expired in 2017 (for failure to pay maintenance fees), which is consistent with there being little or no enforcement activity.
• If you need a definitive answer, the reliable next steps would be: (1) run a party-name search for "Incyte" in PACER/Unified Patents, and (2) run the exact patent number through Docket Navigator, Lex Machina, or Westlaw Litigation Analytics, which I cannot query directly here.

Bottom line: On the evidence available to me, there is no known litigation involving US 6,023,659. I want to be explicit that this is an absence of found records rather than positive confirmation of no litigation ever filed.

I'll verify the structured data against public sources before reporting.

Proceedings overview

Total AIA trial proceedings on file: 0. The USPTO Open Data Portal structured block returns no AIA trial proceedings for US 6,023,659, and my independent web searches surfaced no IPR, PGR, or CBM petition ever filed against this patent — no institution decisions, no Final Written Decisions, no CAFC appeals from the PTAB, and no defensive-aggregator challenges. The breakdown is therefore 0 active / 0 invalidated / 0 sustained / 0 settled / 0 institution-denied. The bottom-line defensive posture is "the claims have never been tested at the PTAB — all 15+ claims (including independent claims 1 and 14) remain presumptively valid but entirely unadjudicated" — a defendant gets neither the benefit of a cancellation it can point to, nor the burden of a hardened patent backed by a PTAB win.

⚠️ Search-noise warning. The letter string "659" recurs constantly in PTAB/CAFC literature, but every hit I found is a different patent. Do not let these migrate into a memo as "prior PTAB history" for your patent:

• PGR2021-00006, Incyte Corp. v. Concert Pharms., Inc., FWD 2022-05-11 — that is U.S. 10,561,659 (deuterated ruxolitinib / hair-loss dosing), later appealed as Incyte Corp. v. Sun Pharm. Indus., No. 2023-1300 (Fed. Cir. May 7, 2025), dismissed for lack of Article III standing.
• IPR on U.S. 9,249,149, institution denied Oct. 2017 — again Concert, again a deuterated-drug patent, not Incyte's database patent.

Neither case involves US 6,023,659, Incyte's protein-function-hierarchy database patent, or any biomolecular-sequence database claim.

Proceedings on file (US 6,023,659)

No AIA trial proceedings on file

• Type: N/A
• Filed: N/A
• Status: No proceedings returned by the USPTO Open Data Portal structured feed as of the most recent ingest; web search corroborates zero PTAB filings.
• Judge panel: N/A
• Petition grounds: N/A
• Institution decision: N/A
• Final Written Decision: N/A — no claim of US 6,023,659 has ever been addressed by the Board.
• Settlement / termination: N/A
• Appeal: None from the PTAB. (There was a district court suit — see below — but no CAFC appeal arising from a PTAB FWD.)
• Defensive value: You cannot build an IPR-estoppel or "claims already canceled" argument, and conversely you cannot be ambushed by an FWD adverse to you. Any invalidity case has to be built from scratch, and any IPR you file would be a first-instance petition on an untested patent.

District-court context (not a PTAB proceeding — noted because it explains the absence)

US 6,023,659 was asserted, which makes the total absence of PTAB activity notable rather than merely a sign the patent was never commercialized. On 2000-08-22, Incyte Genomics Inc. announced two infringement suits: one against Gene Logic alleging infringement of US 6,023,659 ("a database system for storing biomolecular sequence information ... catalogued and searched according to one or more protein function hierarchies"), and one against Affymetrix on U.S. 5,716,785 and U.S. 5,891,636. Source: Bioprocess Online, "Incyte Genomics files two patent infringement suits". The litigation predates the AIA (IPR available Sept. 2012; PGR/CBM Sept. 2012), and by the time AIA trials became available the patent was already deep into its term — it expired on its 2017-03-06 anticipated-expiration date and is recorded as Expired – Fee Related. That is the cleanest explanation for zero PTAB activity: the patent's asserted life and its post-AIA life barely overlapped, and the sole identified defendant's dispute resolved in the pre-AIA era.

Strategic summary

Claim status: everything is UNTESTED. No claim of US 6,023,659 has been canceled, confirmed, or construed by the PTAB. Independent claim 1 (computer system with a first protein-function hierarchy split into a cellular-level set and an above-cellular-level set, plus a user interface) and independent claim 14 (the corresponding method) stand exactly as issued on 2000-02-08, as do dependent claims 2–13 and 15+ (including claim 8's second molecular/enzymatic hierarchy, claim 10's orthogonal-hierarchy query, and claim 13's full-length-project records). There is no U.S. Patent No. 6,023,659 claim that has been narrowed by reexamination, disclaimer, or certificate of correction in any PTAB record I can find. If you are facing assertion, do not assume any claim is weak or strong based on prosecution history alone — there is no adversarial record whatsoever.

Estoppel landscape: no § 315(e)(2) estoppel exists against anyone. Because no IPR/PGR was ever instituted, no petitioner and no privy is barred from raising any § 102/§ 103 ground in a district court or ITC action. A defendant today has the entire universe of prior art available — including Incyte's own pre-1996 product literature, which is unusually rich here: the patent's own file history and the related-patent citations reference Incyte LifeSeq™ Release Notes and Physical Data Models for versions 2.5 (June 1995), 3.0 (Sept. 1995), 3.4 (Jan. 1996), 4.0 (Apr. 1996), 4.1 (July 1996), and 4.2 (Oct. 1996), and a 1996 In Vivo article ("Incyte Serves Up Information, part I"). Those are printed publications with pre-critical-date dates that appear in the same family's IDS material — an obvious § 102(b) starting point that no prior petitioner has burned. Note the equally important availability limit: the patent's priority date is 1996-10-10 (provisional 60/028,284) with a 1996-12-12 provisional and a 1997-03-06 filing date, so pre-AIA § 102/§ 103 applies to any IPR you file — § 311(b) limits you to patents and printed publications, and you cannot use § 112 as an IPR ground (only in a PGR, which is unavailable for a patent with this priority date).

Pattern signals: none of the expected ones. There is no repeat petitioner (no petitioner at all), the patent owner has never pursued a PTAB appeal, and no defensive aggregator such as Unified Patents appears anywhere in the chain. The absence is a genuine signal — well-asserted patents in active commercial disputes reliably attract IPRs, and this one did not, most plausibly because its enforcement window (the 2000 Gene Logic action) closed before AIA trials existed and the patent expired 2017-03-06.

Recommended next steps

• The absence of PTAB activity is itself the finding. State it plainly in any opinion letter: as of 2026-09-11, no IPR, PGR, or CBM has ever been filed against US 6,023,659. Do not let a "659" hit from the Concert/Sun deuterated-ruxolitinib line (PGR2021-00006, FWD 2022-05-11; CAFC No. 2023-1300, dismissed 2025-05-07) be mistaken for history on this patent.
• Check expiration before anything else. The ODP record shows an anticipated expiration of 2017-03-06 and legal status Expired – Fee Related. Before evaluating an infringement theory, confirm the maintenance-fee/expiration posture and any term adjustment; an expired patent cannot support prospective injunctive relief and any damages window is historical. This is likely the single most dispositive fact for a defendant.
• If a demand letter nonetheless cites this patent, treat it as a red flag. Parallel Web Systems-style assertion of an expired, never-PTAB-tested patent should prompt a request for the patent's maintenance-fee history and the specific claims and accused product, and a candidacy assessment for a covered-business-method argument is moot (CBM is sunset for post-2012 filings).
• If you are contemplating an IPR on a still-live related family member instead (e.g., the continuations in the same family, such as U.S. 6,643,634 or U.S. 6,519,583 and the 5,970,500 / 5,966,712 line), note that any such petition is a different proceeding on a different patent and carries no estoppel or outcome from US 6,023,659. Watch for the same early-1990s priority dates and the same LifeSeq Release Notes prior art.
• Verification gap I cannot close from here. I could not retrieve a PTAB E2E docket page or a CourtListener docket for US 6,023,659 (the searches returned nothing and I have no direct E2E/CourtListener API access). My "zero proceedings" conclusion rests on the ODP structured feed plus affirmative absence in web search, not on a direct E2E lookup. If this matters to a filing, pull the E2E Patent Trial search on application number 08/812,290 and confirm before relying on it in a brief.

I'll research the assignment record for US 6023659, focusing on reel/frame data and correspondents of record.

Assignment & Ownership Analysis — US 6,023,659

Scope note / sourcing limitation (read first): The USPTO Patent Assignment Center (assignmentcenter.uspto.gov, formerly assignment.uspto.gov) is an interactive search application and its reel/frame, execution-date, and correspondent-of-record fields are not exposed in the indexed web results I can reach. I therefore reconstructed the chain from (a) the Google Patents legal-events record, which is derived from the same USPTO assignment data, and (b) the printed patent face. I was unable to retrieve reel/frame numbers or correspondent names for either recorded assignment on this patent, and I will not invent them. Where a field is unknown I say so. This is a genuine data gap, not a finding.

Inventors

All eight inventors are listed on the printed patent with California residences consistent with Incyte Pharmaceuticals' Palo Alto, CA headquarters:

Basis for the "employer" column: the patent is assigned on its face to Incyte Pharmaceuticals, Inc. (Palo Alto), and all eight named inventors executed the assignment to Incyte Pharmaceuticals recorded 1997-07-25 (Google Patents legal events). A single blanket assignment executed by all eight is strong evidence of common employment, though I could not retrieve the underlying assignment document to confirm employment recitals.

Pattern notes:

• No departure pattern is visible. I found no evidence that any inventor assigned away from Incyte or that the group scattered. This is the opposite of the "all inventors leave within 12 months" fire-sale precursor. Several of these inventors (e.g., Hillman, Au-Young) are prolific serial Incyte inventors across the mid-1990s genomics families, which is consistent with career in-house staff rather than a one-off group assembled for a single filing.
• Name-spelling discrepancy to flag: the Google Patents assignment record spells the assignor "AKERBLUM, INGRID E." while the printed patent and Google Patents bibliographic data spell the inventor "Akerblom, Ingrid E." One of the two is a typo. This is not an ownership defect, but it is exactly the kind of spelling variance that causes a hit-and-miss result when searching the Assignment Center by assignor name — worth knowing if you re-run the search by name.
• I could not determine whether any inventor executed a separate, individual assignment or whether all eight are covered by the single 1997-07-25 record. The Google Patents entry lists all eight assignor names in one event, which suggests one record.

Original assignee

Incyte Pharmaceuticals, Inc. (Palo Alto, CA) — later Incyte Genomics, Inc. — current listed assignee Incyte Corporation (Wilmington, DE).

• Primary line of business: Incyte was the pioneer commercial genomics-information company. It built and sold large EST and full-length cDNA sequence databases (the LifeSeq™ and LifeSeq FL™ products expressly named in the specification) and derived revenue from database subscriptions and licenses, alongside a later drug-discovery business.
• Did they ship a product embodying the claims? Yes — this is well-evidenced. The specification itself describes the commercial product ("Examples of private internal databases include the LifeSeq™ and LifeSeq FL™ databases available from Incyte Pharmaceuticals, Inc. of Palo Alto, Calif."), and the asserted claims (a database of biomolecular sequence records grouped into a protein-function hierarchy plus a user interface for selectively viewing them) map directly onto that product. Incyte's own public statements at the time of suit described '659 as covering "a database system for storing biomolecular sequence information in a manner that allows sequences to be catalogued and searched according to one or more protein function hierarchies," and Incyte's general counsel called the technology "fundamental to our genomic databases."
• Current status: Operating. Incyte Corporation is a publicly traded, going-concern biopharmaceutical company (NASDAQ: INCY). Incyte's business model changed dramatically after ~2002 — it wound down/discontinued the genomics-information database business and refocused on drug discovery — but the corporate entity that owns this patent never dissolved and never entered bankruptcy.

Assignment timeline

Two records exist in the Google Patents legal-events feed (which mirrors USPTO assignment data). Reel/frame numbers are unavailable from my sources and are shown as "not retrieved."

• 1997-07-25 (recorded; execution date not retrieved — Google Patents records a single date for this event) — Reel not retrieved/Frame not retrieved

  • Conveyance: Assignment ("ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS)")
  • Assignor: Akerblum [sic], Ingrid E.; Altus, Christina M.; Hillman, Jennifer L.; Maslyn, Timothy J.; Seilhamer, Jeffrey J.; Klingler, Tod M.; Au-Young, Janice; Russo, Frank (all eight named inventors, jointly)
  • Assignee: INCYTE PHARMACEUTICALS, INC. (Palo Alto, CA)
  • Correspondent: not retrieved — the Assignment Center correspondent field is not exposed in my sources.
  • Context: Routine pre-issuance assignment of inventors' rights to the commissioning employer; the application was filed 1997-03-06, so the record post-dates filing by ~4.5 months. No third party involved.

• 2001-01-02 (recorded) — Reel not retrieved/Frame not retrieved

  • Conveyance: Change of Name ("CHANGE OF NAME (SEE DOCUMENT FOR DETAILS)")
  • Assignor: INCYTE PHARMACEUTICALS, INC.
  • Assignee: INCYTE GENOMICS, INC.
  • Correspondent: not retrieved.
  • Context: Internal corporate name change only — no change in beneficial ownership, no consideration identified in the record as indexed.

Additional flag — a likely third record I could not confirm: Google Patents' "Current Assignee" field lists Incyte Corp (Wilmington, DE), and the patent's own front-page correspondent address is "INCYTE CORPORATION (WILMINGTON, DE, US)". Incyte Genomics, Inc. later changed its name back to Incyte Corporation, which in the normal course would have generated a further "Change of Name" record on the entire portfolio. I did not see a second change-of-name record in the legal-events feed, and I could not retrieve it. Treat the Incyte Genomics → Incyte Corporation step as probable but unverified from my sources; it should be confirmed directly in the Assignment Center. If it exists, it is another name-change-only record and does not alter the analysis.

What is NOT in the chain (affirmative finding): There is no assignment to any LLC, no assignment to a licensing entity, no security agreement, no merger record, and no post-2001 transfer of any kind in the sources I could reach. A Gene Logic license agreement document exists in the public record (Sections 2.2 and 3.1: "non-exclusive, fully paid up, non-transferable ... world-wide license under the ... Patents," with stipulation of dismissal of the N.D. Cal. actions), but a non-exclusive, non-transferable license is not an assignment and is not a transfer of ownership. Do not let the existence of that contract artifact imply a chain-of-title link — it is not one.

Timeline diagram

timeline
    title Ownership of US 6023659
    1996 : Priority filings Oct 10 and Dec 12
    1997 : Utility application filed Mar 6
         : Inventors assign to Incyte Pharmaceuticals
    2000 : Patent issued Feb 8
         : Incyte sues Gene Logic for infringement
    2001 : Name change to Incyte Genomics
         : Gene Logic action settled by license
    2017 : Anticipated expiration Mar 6

NPE / troll-pattern signals

1. Shell-entity transfer — NOT PRESENT. There is no assignment to any entity at all beyond the two internal records above. No "IP/Patents/Licensing/Holdings/Ventures" suffix appears anywhere in the chain; the terminal owner is a NASDAQ-listed operating pharmaceutical company. No registered-agent service address, no single-purpose LLC, no Delaware/Texas shell.

2. Known asserter in the chain — NOT PRESENT. Neither recorded assignee nor the current listed assignee matches any entry on the standard NPE lists (Acacia, Marathon Patent Group, Intellectual Ventures, IPNav, Wi-LAN, Mosaid/Conversant, Vringo, Pendrell, Innovatio, MPHJ, Lumen View, Round Rock, Document Generation Corp, or Spangenberg-linked entities). The only non-owner with patent rights on this number is Gene Logic, Inc., which received a non-exclusive license, not title — Gene Logic was itself an operating genomics company and the defendant, not an asserter.

3. Repeat correspondent across the chain — UNCLEAR (data unavailable). I could not retrieve the correspondent-of-record field for either 1997-07-25 or 2001-01-02, so recurrence cannot be tested. For completeness, the prosecution correspondent on the patent face is Melanie A. Weinhardt, with the correspondence address given as Incyte Corporation (Wilmington, DE) — but a prosecution attorney of record is a different field from the assignment-record correspondent, and I will not treat the one as evidence of the other. No NPE assertion-list lawyer can be identified on this chain from my sources.

4. Cascading transfers — NOT PRESENT. Two records total across ~four years, and the second is a name change (same corporate person, new name). There is no sequence of chained assignments, let alone multiple transfers inside 24 months or shared correspondent addresses among would-be assignees.

5. Pre-litigation transfer — NOT PRESENT. Incyte sued Gene Logic in the U.S. District Court for the Northern District of California, with complaints reported in December 1999 and August 2000, and settled in early 2001. The only record anywhere near the suit dates is the 2001-01-02 change of name, which (a) post-dates the suit, (b) is a name change, not a transfer, and (c) therefore could not have been arranged to create standing or set venue. The plaintiff at filing and the patent owner were the same corporate person throughout.

6. Bankruptcy fire-sale — NOT PRESENT. No Chapter 7 or Chapter 11 sale of this patent is recorded. The original assignee's corporate successor is an ongoing operating company. Nothing resembling a Kodak/Nortel/Polaroid-style asset sale appears anywhere near this number.

7. Privateering — NOT PRESENT. The one assertion of this patent was brought in Incyte's own name, against Gene Logic, a direct competitor in the gene-expression-database business. That is vertical competitor litigation by the operating owner, the inverse of privateering. No fronting entity, no revenue-sharing NPE, and no SEC disclosure of a "monetization" arrangement is implicated in anything I found.

8. Defensive aggregator — NOT PRESENT. The chain does not terminate at RPX, AST, LOT Network, Unified Patents, or OIN. The terminal owner is Incyte Corporation. The patent was never neutralized by defensive aggregation; it simply ran out.

Verdict

Operating-company assertion.

The chain contains exactly two USPTO-recorded events — the 1997-07-25 assignment of all eight inventors' interest to Incyte Pharmaceuticals, Inc., and the 2001-01-02 "Change of Name" to Incyte Genomics, Inc. (both reel/frame not retrieved; no correspondent retrieved) — with no intervening or subsequent transfer to any licensing entity, and no match to any public NPE roster. Incyte owned and shipped the LifeSeq/LifeSeq FL database that embodies claim 1, and asserted '659 in its own name against Gene Logic, a direct competitor, in N.D. Cal. (complaints reported Dec 1999 and Aug 2000), resolving the matter in 2001 by granting Gene Logic a non-exclusive, non-transferable license — a license, not an assignment. Every one of the eight NPE signals is either not present or (signal 3, correspondent recurrence) unclear solely because the field was unrecoverable. With the patent expired (anticipated expiration 2017-03-06; Google Patents status "Expired – Fee Related"), there is no live assertion risk to assess.

Verification link: https://assignmentcenter.uspto.gov/ (search by patent number 6,023,659) and https://assignment.uspto.gov/patent/index.html.

⚠️ Contradiction flagged against a previously generated section

The earlier "Litigation summary" section states: "No litigation was found involving US Patent 6,023,659 ... no district court complaints ... Bottom line: there is no known litigation involving US 6,023,659." That is wrong, and it contradicts the earlier "Patent summary" section, which correctly identifies Incyte Genomics, Inc. v. Gene Logic, Inc. (N.D. Cal., reported Aug 22, 2000), settled early 2001 with a non-exclusive license. The litigation is corroborated by multiple independent contemporaneous sources (BioCentury, BioProcess Online, and Incyte's own SEC-filed 10-Q language referring to "the lawsuits filed by the Company against Affymetrix in August 2000 and Gene Logic Inc. ... in December 1999 and August 2000," with legal expenses "with Affymetrix and GeneLogic of approximately $2.2 million and $5.6 million in the three and nine months ended September 30, 2000"). My analysis above relies on the "Patent summary" section as the authoritative account for this patent and treats the "Litigation summary" section's negative finding as an error — most likely a search-syntax failure (searching the "'659" shorthand, which collides with the unrelated US 10,561,659 ruxolitinib patent).

Other flags carried forward

• Do not conflate US 6,023,659 with US 10,561,659. The ruxolitinib dosing patent (PGR2021-00006; Incyte Corp. v. Sun Pharmaceutical Industries) and the 2026 Incyte v. Zydus / Alkem matters are a different patent family entirely.
• Status label nuance: Google Patents shows "Expired – Fee Related" with an anticipated expiration of 2017-03-06, which is exactly 20 years from the 1997-03-06 filing date. A full 20-year term would normally be labeled simply "Expired," so the "Fee Related" qualifier may reflect a maintenance-fee lapse at the 12-year window — or may be an artifact of Google's status mapping. I did not verify the maintenance-fee payment history and cannot confirm which it is. Either way, the patent is long past its enforceable term.
• Reel/frame and correspondent data for this patent remain unretrieved. If you need them, the Assignment Center's per-record detail view (and the "Correspondent" column in its results grid) is the authoritative place to look, and a PAIR/Patent Center continuity-data pull will cross-check the same records.

I'll research the prior-art citations for this patent. Let me run several targeted searches.

I found the front-page references. Let me dig deeper to get the complete "References Cited" list from the patent PDF and Google Patents citation section.

USPTO prior-art search — US Patent No. 6023659

0. Important upfront notes (data provenance & a flagged contradiction)

Confirmation of the patent. The number you gave, 6023659, resolves to US 6,023,659 B1, "Database system employing protein function hierarchies for viewing biomolecular sequence data," Incyte Pharmaceuticals, Inc., filed 1997-03-06, granted 2000-02-08, app. 08/812,290 (source: the patent's own front page and Google Patents, https://patents.google.com/patent/[US6023659A](/patent/US6023659A)/en). The prefix "US" and B1 kind code are added only as bibliographic formatting; the identifier itself was not altered.

⚠️ Contradiction between the two previously-generated sections. The "Patent summary" section states Incyte's Gene Logic suit over 6,023,659 settled in early 2001, while the "Litigation summary" section states no litigation was found. My searches this session returned positive corroboration of the Gene Logic suit on 6,023,659:

• BioCentury: Incyte settled N.D. Cal. suits alleging infringement of U.S. Pat. Nos. 5,716,785, 5,891,636 and 6,023,659; Gene Logic received a non-exclusive license; "'659 covers a database system for storing biomolecular sequence information" (https://www.biocentury.com/article/[118713](/patent/118713)/...).
• The Free Library / Incyte press release reproduces the same list including 6,023,659 (https://www.thefreelibrary.com/Incyte+licenses+comprehensive+microarray+patent+portfolio+to+Chiron.-a071900983).

So the "Litigation summary" section's "no litigation" conclusion is the one that should be corrected; the "Patent summary" section is consistent with the search results. (Note these searches also confirm the "'659" false-match warning: PGR2021-00006 concerns US 10,561,659, an unrelated ruxolitinib dosing patent, and must not be conflated with 6,023,659.)

⚠️ Limitation on completeness. I was not able to open a live USPTO Patent Public Search / Patent Center record this session; I worked from the patent's own front page (the USPTO-printed PDF: US6023659.pdf, hosted at patents.google.com/patentimages, file 58/da/70/18bc339fc5f7d0/US6023659.pdf) and the Google Patents bibliographic page. The "References Cited" block I could retrieve is partial (the OCR/search snippet begins at 5,418,944). There may be additional U.S. patent references above/below the ones shown that I did not capture. Do not treat the list below as the complete examiner citation list until you confirm it against the "Citations" tab on Google Patents or the PDF front page directly.

1. References Cited (patent citations) found on the 6,023,659 front page

These are the backward ("References Cited") citations — i.e., the art cited against 6,023,659 during prosecution.

Non-patent reference cited:

Honesty flags on the reference details. Per your strict rule and my operating rules: I know the numbers, dates, and examiner-assigned classes because they appear on the patent front page. I cannot confirm from the retrieved material the titles, abstracts, or claim content of US 5,418,944 / 5,523,208 / 5,706,498. I am therefore deliberately not inventing descriptions of what those patents disclose. To fill those fields you must pull each patent's front page (USPTO Patent Public Search, or Google Patents for 5,418,944 / 5,523,208 / 5,706,498).

Also note: the forward citations ("cited by," e.g., Affymetrix US 6,420,108; Sangamo US 7,923,542, per the prior sections) are later documents and are not prior art to 6,023,659 — they may only be relevant as evidence of the field, not for § 102.

2. § 102 anticipation analysis (claim-by-claim mapping)

The claims to test are the independent claims 1 (computer system: database + first hierarchy of biological function categories spanning a cellular level and a level above cellular + user interface), 14 (sequence→categories method), 21 (categories→sequences method), and 27 (database: sequence records with external-database hit references + external-hit records that reference protein-function hierarchy categories), plus dependents (e.g., claim 8 second/molecular-enzyme hierarchy; claim 9 EC list; claim 10 cross-hierarchy query; claim 13 projects; claim 7 tissue/organism-level categories).

Two governing caveats before the mapping:

• Citation ≠ anticipation. A reference the examiner cited is presumptively the closest art, but this patent issued, meaning the examiner necessarily found each cited reference did not anticipate/disclaim the allowed claims. Anticipation under § 102 requires a single reference disclosing every element as arranged in the claim (no missing element, no unstated but inherent disclosure).
• Because I could not verify reference content, the mapping below is which claims each reference would be evaluated against, not a finding of actual anticipation.

Bottom line on anticipation. On the record available, none of the cited references appears to disclose the single most distinctive element that carried these claims to allowance — an automatically populated hierarchy of protein-function categories distinguishing biological function (with a cellular level and an above-cellular level, e.g., tissue/organism) from molecular/enzyme function, together with external-hit records that reference those hierarchy categories (the FL_PFExternalHit linkage in the FIG. 3 data model) and a user interface that queries in either direction (sequence→category, claim 14; category→sequence, claim 21). The cited art in classes 702, 435/6, and 395/606 addresses data processing, nucleic-acid testing, and generic database access, respectively — i.e., it is background/ancillary art, not a systemic anticipation of the hierarchy-centric claims. That is consistent with the patent's issuance, the specification's own statement that "this area of technology is still in its infancy," and the fact that the patent was later asserted (Incyte v. Gene Logic) and licensed.

3. What I could not do (explicit)

1. Query the USPTO Patent Center / Patent Public Search interface directly for 6,023,659 — unavailable in this session; I used the patent's official printed front page (patentimages PDF) and Google Patents. The number was not auto-corrected and no similar number (e.g., 6,023,669; 10,561,659) was substituted.
2. Verify the titles/abstracts/disclosures of US 5,418,944, 5,523,208, and 5,706,498. I will not fabricate those.
3. Confirm the complete "References Cited" list. The retrieved list may be missing additional cited U.S. patents; verify against the PDF front page or Google Patents "Citations."
4. My searches hit a step limit before I could retrieve the Google Patents "Patent Citations" table in full; the last two queries returned step-limit errors, not substantive results.

Recommended verification path: (a) open https://patents.google.com/patent/US6023659A/en and click Citations for the full backward-citation list; (b) open each cited patent on USPTO Patent Public Search to capture title/abstract/claims; (c) confirm the front-page reference list against the issued PDF (US6023659.pdf, patentimages file 58/da/70/18bc339fc5f7d0/US6023659.pdf).

I'll ground this analysis in the actual prior-art references of record and contemporaneous (pre-1997) bioinformatics systems. Let me search.

Let me pin down the actual "References Cited" (patent and non-patent) of record for US 6,023,659.

Obviousness Analysis — US 6,023,659 under 35 U.S.C. § 103

0. Sourcing note and a flagged contradiction (read first)

What I could and could not verify. The Google Patents text supplied to me is truncated mid-Description (it ends at "...if the user selects the description (i.e., step 460 is answered in the affirm"), so the page's "References Cited" / "Patent Citations" section and the claim set were NOT delivered in the provided text. My follow-up searches surfaced only forward citations ("Cited By") to '659, not '659's own prior-art-of-record list. (One aggregator, expertkg.com, displays "Citations | 78" but does not enumerate them.) I therefore cannot and do not represent the following as "the references of record." What follows is built from three verifiable tiers:

1. Admissions in the patent itself (self-identifying prior art — the strongest evidentiary posture for a § 103 challenge);
2. The "Prior art keywords" block listed on the page (sequence, sequences, database, protein, records), plus CPC classes G16B50/00, G16B20/00, G16B30/00;
3. Pre-1997 public systems I confirmed by search (URLs below).

⚠️ Contradiction between the two prior sections. The "Patent summary" section states that Incyte Genomics, Inc. v. Gene Logic, Inc. (N.D. Cal., ~Aug. 2000) asserted 6,023,659 and settled in early 2001 with a non-exclusive license. The "Litigation summary" section states no litigation was found. These cannot both be right. The "Patent summary" account is the more specific (it names a court, a date, and a license instrument), so I treat it as the better-supported version pending a Docket Navigator/Lex Machina check — but I flag it as unresolved. This matters here only for secondary considerations (§ IV.B below).

(Minor: the system clock reads 2026-09-11; the task header reads 2026-04-26. Not material to the analysis.)

I. Claim decomposition (from the authoritative text retrieved)

Key dependents: 7 (organism/tissue-level categories), 8 (second hierarchy: molecular and/or enzymatic), 9 (second hierarchy = Enzyme Commission list), 10 (cross-hierarchy querying), 12 (sequence → its categories), 13 (linkage to full-length gene "projects"), 16 (organism-level set in the method claim).

Critical scope observation. The specification's most distinctive disclosure — the keyword/anti-keyword automatic classification algorithm (Definitions section; FIGS. 6A/6B) — is not recited in any claim. The claims are directed to (a) a hierarchical controlled vocabulary, (b) a record-level mapping between sequence records/hit records and that vocabulary, and (c) a conventional query/report user interface. That is important: the "hard part" of the disclosure is unclaimed, while the claimed subject matter sits squarely in the field's ordinary toolkit. Note also the page's own prior-art keyword block — sequence, sequences, database, protein, records — i.e., the claims are drafted in the field's most generic vocabulary.

II. Prior-art reference set (with confidence and provenance)

Tier 1 — admitted prior art in the '659 specification (no search risk):

• GenBank / GenPept and associated NCBI databases — expressly named as the "external database," including genbank-rodent (gbrod) / primate (gbpri) partitions. Same for the Blocks database (Fred Hutchinson) and the Swiss-Prot site (Univ. of Geneva).
• The Enzyme Commission enzyme list ("EC list"), "as provided by the Enzyme Commission and maintained at the Enzyme Nomenclature Database at the Swiss-Prot site." Claim 9 claims this list. A reference that the patent expressly incorporates as pre-existing is prior art by admission.
• BLAST and the Smith-Waterman algorithm, with the patent's own scoring parameters and "HSP"/"BLAST Score"/"P-value" outputs — i.e., the admitted mechanism for generating the "hits" recited in claim 27.
• Incyte's own LifeSeq™ / LifeSeq FL™ relational databases — the specification admits "relational database systems such as those developed by Incyte Pharmaceuticals, Inc. provide great power and flexibility" and that new sequences are BLASTed against public databases and "annotated based on located matches ('hits')."
• Oracle™ / Sybase™ commercial RDBMSes and a UNIX + World Wide Web server/browser client–server architecture (FIG. 2A) — the specification treats all of this as off-the-shelf.

Tier 2 — pre-1997 public systems confirmed by search:

• Entrez / WWW Entrez (NCBI). Epstein, Kans & Schuler, WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology (2nd WWW Conf., 1994) — https://files.eric.ed.gov/fulltext/ED462262.pdf. Confirmed content: an integrated molecular sequence retrieval system over nucleotide and protein databases including GenBank plus MEDLINE; user selects database → field → query terms; "selection mode" lets users scroll hierarchical alphabetical term lists when they don't know the exact term; Boolean queries across separately indexed fields; inter-database "links" (e.g., mark MEDLINE articles → retrieve related sequence data) and intra-database "neighboring"; and hypertext representation of the hierarchical organism taxonomy. NCBI's own description of the Entrez engine (indexing fields, DocSums, links/neighbors, common retrieval engine across source databases): https://www.ncbi.nlm.nih.gov/books/NBK21081/
• SRS (Sequence Retrieval System). Etzold & Argos, SRS — an indexing and retrieval tool for flat file data libraries, CABIOS 9(1) (1993) — https://www.semanticscholar.org/paper/96f3bb55c09d1c49d59698e9d89495c14cf83aee ; plus the 1992 EMBnet deployment announcement — https://bio.nic.funet.fi/pub/sci/molbio/historical/biodocs/srs.gopher. Confirmed content: keyword retrieval "on the documentation of the sequences" from EMBL, SwissProt, PIR; the databases are "cross-linked" (an EMBL hit can be used to retrieve the referenced SwissProt entry); and a secondary database layer including "ENZYME (A. Bairoch)", PROSITE, EPD, ECD, TFD, REBASE searchable "either on their own or in conjunction with the primary databases."
• SRS field-limited, cross-linked query syntax (1995). https://bio.net/bionet/mm/bio-srs/1995-March/000023.html — documented queries of the form get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot kinase.pep, i.e., select a functional category → return all sequences linked to it, and then >pdb (chain to a further linked database).
• WWW-Query. Perrière & Gouy (1996), a WWW retrieval system for EMBL/GenBank/DDBJ nucleotide and NBRF/PIR protein banks (surfaced in the SRS citing literature).

Tier 3 — training-data recollections NOT confirmed by the searches I ran (search budget exhausted; flagging per the "do not fabricate" rule): published multi-level functional classifications of gene products — e.g., Monica Riley's functional catalog of E. coli gene products (1993, Microbiol. Rev.); TIGR "role categories" (mid-1990s); WIT/PUMA (Argonne) hierarchical functional classes; KEGG (Kyoto, 1995). If any one of these is verified and dated before October 1996, it supplies the "above-cellular / tissue / organism level" limitation directly, and the analysis below collapses to a two-reference combination.

III. Combinations rendering the claims obvious

Combination 1 (primary rejection) — Entrez + SRS + ENZYME/EC list + a multi-level functional classification

The only element not literally met by a single Tier-1/2 reference is Claim 1's requirement that the same biological-function hierarchy contain both cellular-level and above-cellular-level categories. That limitation is met either by a Tier-3 functional classification, or by the combination of Entrez's organism-taxonomy node with the EC hierarchy — i.e., it is supplied by combining two hierarchies that the art already used together.

Combination 2 — Swiss-Prot/GenBank annotation + BLAST hit records + EC/functional keywords (directed at claim 27)

Claim 27 needs only: sequence records → external-hit records → function-category references. Swiss-Prot already carried (a) a controlled KW keyword field, (b) DR cross-references to other databases including ENZYME, and (c) sequence → function annotation; BLAST produced the "hits"; the patent admits that its own records store "Hit_ID, Hit_Type, Hit_Description, Hit_DataSource, PFHit_YN." Mapping hit records to an existing function vocabulary is the entire claim. This is the single strongest anticipatory-flavored combination; claim 27 is vulnerable even to a two-reference attack (Swiss-Prot/GenBank + ENZYME), because claim 27 says "at least one of biological or molecular functions" — a disjunctive limitation satisfied by molecular/enzymatic function alone, which the EC hierarchy provides verbatim.

Combination 3 — the "two-way mapping" UI claims (14, 21)

Every structural element of these claims is a known database query/report paradigm: (i) render a list, (ii) capture the user's selection, (iii) resolve the selection against a mapping/join, (iv) render results. Entrez's "selection mode → Boolean query → DocSum list → double-click to view record" and SRS's field:value > linked-database idiom are the same four steps pointed at a category axis instead of an organism/author axis. Substituting a curated function taxonomy for an organism or author taxonomy is a predictable substitution of one data field for another.

IV. Why a person of ordinary skill would have combined these (KSR factors)

A. The problem was known and pre-identified. The specification itself states the motivation: EST programs were generating large numbers of partial sequences whose function was unknown; existing relational systems were powerful but "in its infancy," and "further improvements ... will help accelerate biological research." A § 103 analysis begins from a skilled artisan confronting exactly that problem — and the prior art (Entrez, SRS) had already answered the retrieval half of it.

B. The building blocks were known, and the art taught using them together. SRS's verified 1992–1995 behavior — searching ENZYME, PROSITE, EPD, ECD alongside EMBL/SwissProt/PIR and cross-linking between them — is not merely a suggestion to combine; it is the combination already made. Entrez likewise already integrated sequence and bibliographic nodes with hypertext hierarchy browsing. The patent's contribution over those systems is the choice of organizing axis (protein function) and the curation of the taxonomy.

C. Predictable results / design choice. Implementing a second controlled-vocabulary axis in an extant RDBMS with an extant web front end, using an already-existing, already-multi-level enzyme hierarchy (EC) as the template, is the sort of "combination of familiar elements according to known methods [yielding] predictable results." Nothing in the specification alleges an unexpected technical effect, a superior data structure performance characteristic, or a result that a skilled artisan would not have expected — the disclosed benefits are all catalogue-and-search benefits that Entrez/SRS already delivered on other axes.

D. Express teaching/enablement of the taxonomy design. The patent describes the "organizing principle" of the hierarchies — "Why" (biological), "What" (molecular), "Where" (tissue/subcellular), "When" (temporal/developmental) — and then itself supplies the roadmap for the claimed hierarchy: "an example of a cellular level category is DNA repair, an example of a tissue level category is apoptosis, and an example of an organism level category is development." Assigning categories at multiple levels of biological organization was therefore not an unrecognized insight but the standard practice of cataloguing; the EC list (4 levels), MeSH tree structures, and organism taxonomies all confirm that multi-level, multi-axis categorization in a retrievable database was routine.

E. No teaching away. Nothing in Entrez, SRS, or the EC material disparages querying sequence collections by protein function or by biological role; the EC list's whole purpose is to make enzymatic function machine-retrievable, and SRS's purpose is to make secondary databases (including ENZYME) searchable in conjunction with sequence libraries.

F. § 112-adjacent evidence of breadth cuts toward obviousness. The claims are considerably broader than the disclosed embodiment: the specification's genuinely non-routine contribution (the keyword/anti-keyword automatic categorizer) is nowhere claimed. A claim that omits the disclosed point of novelty and recites only the known schema + known UI is, a fortiori, more likely to read on the prior art.

Doctrinal hook (argument, not certainty): where a claim's asserted novelty resides in the content and arrangement of non-functional descriptive labels (here, protein-function category names and their parent–child nesting), a challenger will argue under In re Gulack / In re Ngai that the hierarchical arrangement cannot impart patentability to an otherwise conventional database system; the patentee's best rejoinder is the In re Lowry line (a data structure that defines inter-record relationships and enables faster/more accurate searching is functional). Claim 27, drafted as a database structure, is where that fight would be fought — and it is also the claim most exposed under § 101 (Alice, abstract idea + generic computer), a vulnerability the § 103 analysis should be read alongside, not instead of.

V. Secondary considerations

• Licenses. If the Gene Logic license described in the "Patent summary" section is the license-in-settlement of the N.D. Cal. action, it is weak evidence of nonobviousness: a license taken to settle pending litigation, at undisclosed terms, carries little probative weight absent evidence of an independent commercial driver.
• Commercial success. Incyte's LifeSeq™ and LifeSeq FL™ were substantial commercial products, but success would have to be shown to nexus to the claimed multi-level hierarchy rather than to Incyte's sequencing scale, library depth, or data exclusivity.
• Long-felt need / failure of others. No evidence located. And the "need" (function-oriented browsing of sequence data) was at least partially met pre-1996 by Entrez's taxonomy node and SRS's ENZYME cross-linking.

VI. Bottom line and confidence

• Claims 27 (and, a fortiori, dependent claims reciting molecular/enzymatic hierarchies such as 8 and 9): highest § 103 exposure. A combination of a public sequence database with cross-reference/annotation fields (Swiss-Prot/GenBank, or Entrez's cross-node "links") with the Enzyme Commission hierarchy — which the patent itself admits is prior art — discloses every element, including the disjunctive "biological or molecular" limitation.
• Claims 1, 14, 21: strong § 103 exposure, conditioned on the "cellular level + above-cellular level" limitation. Entrez + SRS + ENZYME meets everything else literally, and the multi-level requirement is met by (a) any verified pre-Oct-1996 multi-level functional/role classification (Riley, TIGR, WIT, KEGG — unverified here), or (b) the combination of Entrez's hierarchical organism taxonomy with the EC hierarchy, or (c) a Gulack-style holding that the taxonomy's arrangement is non-functional descriptive matter that cannot confer patentability.
• Confidence: High on the legal framework and on Entrez/SRS/ENZYME as qualifying prior art (search-confirmed, with URLs). Low-to-moderate on the identity of the specific references the examiner actually applied, because the "References Cited" list of US 6,023,659 was not present in the source text I was given and I could not retrieve it. Before filing any paper, pull the actual front-page references and the file wrapper (USPTO Patent Center / Global Dossier) and re-run this mapping against the applied art; also verify the Tier-3 functional-classification references and their dates, since a verified pre-October-1996 hierarchical biological-role scheme would make Combination 1 a clean two-reference case.