current sequence listing process for nucleic acids and polypeptides dave nguyen technology center...
TRANSCRIPT
Current Sequence Listing Process for Nucleic Acids and
Polypeptides
Dave NguyenTechnology Center 1600
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Current Sequence Listing Process
Technology Center 1600 (TC 1600) is a primary stakeholder in the current sequence listing process and is taking a major role in
– Conducting Automation Workgroup Meetings (AWG) on a biweekly basis to sustain the USPTO business function of performing quality searching of molecular sequences by TC 1600
– Sustaining the PTO's best business practices for processing genetic sequences claimed in patent applications
– Continuing to improve our business process for maintaining the infrastructure for processing molecular sequence listings and searching genetic sequences from applicant submissions and commercial databases of published sequence listings.
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EFS - Web1. Paper only
- PDF file2. CRF / (paper)
- TXT file
Online filing
MAI L1. "Paper" copy
a. CD in lieu of paper (TXT file)
b. Paper2. CRF - TXT file
a. CDb. Floppy
Electronic Sequence Listing Supply Chain
NCBI - COTSConverts pep & seq files
to ASN.1 records
PAIR1. Paper --> TIF2. CRF --> TXT and paper
CRF/SCORE creates up to 3 files:.raw (original data).pep (protein data in IG format).seq (nucleic data in IG format)
Can access Patent & PG Pub (Pre-Grant Publications) w/ sequence listings but cannot search sequence listing
Ask for Revalidation
Publication
Interface for public & applicants to access IFW & SCORE databases
ASN.1 files
Scan the application including Sequence listing.
Manually load
Sequence listing
Automatically load Sequence listing
Automatic load
Raw sequence listing
Manually ftp the filesto ABSS /crf/work/
fixable errors?
Not in Compliance
Manually try to fix formality errors
Yes
No
Run the files throughCRF or SCORE
CRF/SCOREpassed?
No
Patent & PG PUB
CRF/ SCOREdBase
ABSS Search System
PSI PSStore .txt files of mega sequence
listing
GenBank Store all existing sequence listings
Artifact
Search Environment
EAST/WEST Search System
App FT/ Pat FT(Search System)
Yes
VALIDATION
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New Application Received(OPAP)
Mail/CRF Processing;
Palm Initialization; Indexing
and Scanning
(OPAP)
NO CRF, IFW
(OPAP)
Review
(TC 1600)
PLRC:Load CRF in
SCORE
STIC:CRF review (1st pass)
CRF review (2nd pass)
TC1600
1st CRF accepted
CRF rejected
Notice Mailed
OPAP
CRF Needed
No replyNo reply to
form
2nd round of CRF
2nd CRF accepted
2nd CRF rejected
Export to ABSS STIC: ABSS
search
RETURN to
OPAP
CRF Needed
ABN
STIC:CRF review 1st CRF accepted
Export to ABSS
OPAP (Office of Patent Application Processing) Process Map
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New Application Filed in OPAP
CRF BadOPAP sends Sequence Compliance Letter and CRFD to applicant
New Pat.Application
CRF GoodInfo. (CRFE) entered in System (PALM), Application sent for examination
Applicant prepares New Sequence listing
Office (SCORE/STIC) processes New Sequence listing
Office records CRF (Good/Bad) statement as CRFE or CRFDOPAP
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New Application in TC1600 (Status 20 or 25)
CRF Bad sequence disclosed but NO CRF
TC1600
New Pat.Applicationin TC1600
CRF GoodInfo. (CRFE) entered in System (PALM), Application sent for examination
Applicant prepares New Sequence listing
Office (SCORE/STIC) processes New Sequence listing
Office records CRF (Good/Bad) statement as CRFE or CRFD
OPAPOPAP sends Sequence Compliance Letter and CRFD to applicant
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SCORE (Supplemental Complex Repository for Examiners)
System Architecture Diagram
DMZ
Internet
`
PTONET
`
Edge (LINUX) Server
Load Balancers
Edge (LINUX) Server
Load Balancers
HTTP (LINUX) Server
Web Servers
HTTP (LINUX) Server
Web Servers
z
(***) WebSphere 6.1.0.5
Web App Server
(***)
SCORE AIS
ScoreWSWeb
ScoreXMLWeb
ScoreAccessWeb
OIPE LOAD
Content Management
Server1
Oracle Database
Content Management
Server2
Duncan
Doc3
STIC Review
`
eDAN Users
STIC examiners
`
OIPE Load users
Web App Server
(***)
Doc1
Private/Public PAIR Users
SCORE Imports/Exports
Duncan
SCORE import/ export
server
`
SCORE Tech
ABSS RTIS NCBISI-INTL
Import
STIC
ExportExportExport/Import
Rhino1
Rhino2
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Sequence Listing Data Flow: Processing on ABSS
Application docs are separatedfrom the media with files
Manually copy files from mediato local storage
Manually run the files throughCRF or SCORE
CRF/SCOREpassed?
CRF/SCORE creates up to 3 files:.raw (original data).pep (protein data in IG format).seq (nucleic data in IG format)
Applicant mails in patent applicationdocuments and media with files
fixable errors?
Not in Compliance
Manually try to fix formality errors
no
yes
yes
media with files
no
Copy the .pep and .seq filesto ABSS
ABSS (Automated Biotechnology Sequence Search System)
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What Sequence Rules Apply?
• US Rules - 37 CFR 1.821-825– Original rules -- 55 Fed. Reg. 18230 (May 1,
1990) (effective October 1, 1990)– Amended rules -- 63 Fed. Reg. 29620 (June 1
1998) (effective July 1, 1998).• International Rules - WIPO Standard ST.25,
effective July 1, 1998– http://www.wipo.int/standards/en/pdf/03-25-
01.pdf
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Common Compliance Issues
The organism of each sequence must be defined atheading <213> (Organism) (37 CFR 1.822(b))
Genus/species or “artificial sequence” or “unknown”must be used at heading <213>
– Use Genus/species if at all possible• If it is a human sequence, for example, use Homo
sapiens• Depends on source of the actual sequence
– If artificial sequence or unknown, further definition is required at headings <220> - <223>
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Common Compliance Issues
Artificial Sequence at heading <213>?
Explain why the sequence is artificial
(not naturally-occurring) If a portion of the sequence was derived from a natural
source, e.g., a bacterial gene, then provide the source and
explain how the sequence differs from the naturally
occurring source material
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Common Compliance Issues
Unknown– Use if there is no scientific name disclosed or only
a partial scientific name, e.g., Bacillus sp.– Use if only the source of the organism is
disclosed, e.g., “soil sample from Pittsburgh”– Example sequence listing section:
• <213> Unknown
• <223> Bacillus species
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Sequence Listing Examples
Example 1 Example 2
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Common compliance issues
Sequences having a gap or gaps must be displayed as separate sequences in the Sequence Listing.
For example, if a chemical moiety has several strands of protein attached to it, each protein sequence should appear in the Sequence Listing separately. The chemical moiety should NOT be shown (37 CFR 1.822(e))
Sequences made of fragments of other sequences must be displayed as separate sequences in the Sequence Listing (37 CFR 1.822(e))
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Common compliance issues
Sequence Listings are often non-compliant because of minor formatting issues- Use of PatentIn minimizes such occurrences
PatentIn’s “Copy to Disk” function results in loss of hard returns on the CRF - Regenerate the Sequence Listing and use
Windows Explorer to copy the text file to the CRF
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Filing option
• Electronic Filing System (EFS) - Legal Framework:http://www.uspto.gov/patents/process/file/efs/guidance/New_legal_framework.jsp
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Filing option
• Electronic Filing System (EFS)– Learn about EFS at this website:
http://www.uspto.gov/ebc/efs_help.html • Add the sequence listing to your EFS-Web submission• No paper copy or statement needed for initial filing
– If filing in response to a Notice to Comply a statement that there is no new matter is needed.
– Sequence listing is automatically processed by SCORE and immediately placed in ABSS (if compliant)
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Why does my CRF has an error on Field Code <213>?
Numeric identifier <213> is something other than “Scientific name, i.e., Genus/species, Unknown or Artificial Sequence”
FAQs
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Why does my CRF has an error on Field Code <223>?
A major reason for noncompliance is that theinformation provided in field <223> to explain anartificial or unknown organism is improper.
Solution:Indicating what the artificial sequences are isacceptable, e.g., primer, aptamer, linker, adapter,cloning vector, expression vector, siRNA, probe, expressedsequence tag, etc. Chimeric constructs should identify sourcesof the parts, etc.
FAQs
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FAQs
• Do genes identified by gene accession numbers in the specification need to comply with the sequence rule requirements?
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FAQs
No, they are not considered disclosures of
Sequences.
When accession numbers appear in claims,
they may raise an issue of improper
incorporation of essential material by reference.
If the sequences need to be brought into the
disclosure then they must comply with the
sequence rules.
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FAQs
A sequence listing was prepared via PatentIn.Why did the sequence listing submission getrejected by the Patent Office?
The USPTO uses an in-house verificationsoftware for validation. In addition,information provided in field <223> forartificial sequence or unknownorganism must be manually verified.
