J 7/11 - Just Write It!

Biotech specialists, you might find this decision interesting!

The applicant filed an appeal against the decision of the Receiving Section (RS) refusing the application for lack of compliance with R 30(3).

The application had been filed electronically on September 28, 2010. The description contained a sequence protocol concerning 17 nucleotide and amino acid sequences.

On November 3, 2010, the RS sent form 1128 requesting the applicant to remedy deficiencies pursuant to R 30(3) because elements that were mandatory pursuant to WIPO standard ST.25 had not been supplied. In an annex to the form, the following was stated:

“1) When checking the paper version of the sequence protocol, the following deficiencies have been found:

The numeric identifiers <220>, <221> and <223> are missing. In case of a “artificial sequence “ or if the organism is “unknown”, the mandatory numeric identifiers <220>, <221> and <223> always have to be provided.

<213> artificial sequence (or “unknown”)

<220> (leave empty)

<221> source

<222> (1)..(last position)

<223> /note=“...“ (description of the artificial sequence)

2) In sequence protocols which are filed upon request of a competent office or after having been allocated an application number the following data elements are to be integrated:

<140> current patent application

<141> current filing date

3) The diskette that has been filed does not contain a sequence protocol.”

On November 11, 2010, the applicant filed an amended sequence protocol and explained in an accompanying letter which amendments had been carried out. He had inserted the numeric identifiers <223> for certain features of sequences 1 to 8, which concerned artificial sequences. For sequences 9 to 11, the designation “artificial sequence” in numeric identifier <213> had been replaced by plasmid designations such as “GeneArt plasmid 0908426_256_pMA”, which had already been used in the original description. Moreover, the applicant made the statement that the amended sequence protocol did not contain anything going beyond the original application and paid the fee for the late payment of the sequence protocol.

In a telephone interview which apparently took place on January 21, 2011, the applicant was informed that the sequence protocol did not give the description of the artificial sequences and that some of the feature keys used for the numeric identifier <221> could not be acknowledged.

On January 26, 2011, the applicant filed another sequence protocol using modified feature keys for numeric identifier <221>.

On February 22, 2011, the RS decided to refuse the application. The RS used form 1088S and ticked the following pre-printed text:

“The deficiency (or deficiencies) regarding the sequence protocol, mentioned in the communication pursuant to R 30(3)/R 163(3) (EPO form 1128), has (have) not been remedied in due time or form, respectively.”

The representative of the applicant called the EPO on February 24, 2011 and requested clarification of the deficiencies. He also criticized the defectiveness of the communication dated November 3, 2010.

The applicant then filed an appeal as well as a modified sequence protocol. The statement of grounds of appeal pointed out the following:

• According to the applicant, the communication dated November 3, 2010, was completely incomprehensible. Two of the allegations of deficiencies were incorrect. The general allegation that certain numeric identifiers were missing was not true either. The WIPO standard did not stipulate a duty to provide information with numeric identifier <221>, not even for artificial sequences.
• In a telephone interview several amendments had been discussed. This resulted in the amended sequence protocol filed on November 11, 2010. It is only during a later telephone interview, which took place on January 21, 2011, that the EPO explained that for field <221> only  indications found in Tables 5 and 6 of Annex 2 of standard ST.25 were acceptable. The applicant then filed an amended sequence protocol. The decision to refuse the application referred to the communication dated November 3, 2010 and, therefore, did not contain correct and comprehensible reasons for the decision.
• Moreover, it had been discovered that the sequence protocol filed on January 26, 2011, was deficient, due to a software error of the PatentIn 3.5 software recommended by the EPO. This explained why the applicant had filed yet another amended sequence protocol.
• The appeal fee was to be reimbursed because there had been substantial procedural violations affecting the decision to refuse and also because the principle of the protection of legitimate expectations and the right to be heard had been violated.

Here is what the Legal Board of appeal had to say on this case:

*** Translation of the German original ***

[2] Pursuant to R 30(1) EPC, if nucleotide or amino acid sequences are disclosed in the EP application, the description shall contain a sequence listing conforming to the rules laid down by the President of the EPO for the standardised representation of nucleotide and amino acid sequences. Further rules concerning this matter are found in the Decision of the President of the EPO dated 28 April 2011 on the filing of sequence listings (OJ EPO 2011, 372) which has entered into force on June 1, 2011 and which, according to its Article 8, applies to all European patent applications pending on that date. In principle this Decision also applies to the present case; however, it has to be taken into account that, according to general intertemporal principles, the correct course of the proceedings before the RS has to be assessed on the basis of the legal situation existing at the relevant point in time (in this context, see decisions G 1/07 [1.1] and J 10/07 [1.2]). Insofar the rules of the Decision of the President of the EPO dated 12 July 2007 concerning filing of sequence listings (OJ EP0 2007, special edition 3, C.1), in its version as amended by the Decision dated 26 March 2010 (OJ EPO 2010, 328) are relevant.

[3] According to Article 1(1) of the Decision dated 12 July 2007, the description shall contain a sequence listing complying with WIPO Standard ST.25. This standard concerns the representation of nucleotide and amino acid sequence protocols in applications and has to be applied in its amended version adopted on October 20, 2009 (Article 2 of the decision to amend dated March 26, 2010 has abrogated the Annex of the decision dated July 12, 2007, which contained the previous standard adopted on March 28, 1998)

[4] The sequence protocol filed by the applicant on the date of filing did not comply with WIPO standard ST.25 in two respects.

First, for a great number of sequences (n° 1 to 8 and n° 12 to 17) it used abbreviated designations (such as “ampR”, “ori”, “ScURA3”, “HARS1” etc.) for the numeric identifier <221>, which abbreviated designations did not correspond to the feature keys foreseen in Tables 5 and 6 of Annex 2 of WIPO-standard ST.25.

Secondly, sequences n° 9 to 11 were designated as “artificial sequence” in numeric identifier <213> but the then required data elements <220> (feature) und <223> (other information) were not given (see point 30 of WIPO standard ST.25).

Therefore, the sequence protocol was deficient.

[5] Where the applicant has not filed a sequence listing complying with the requirements under paragraph 1 at the date of filing, the EPO shall invite the applicant to furnish such a sequence listing and pay the late furnishing fee (R 30(3), first sentence). Moreover, R 30(3), second sentence, provides that if the applicant does not furnish the required sequence listing and pay the required late furnishing fee within a period of two months after such an invitation, the application shall be refused. The two-month period is not extendable (see Article 2(1) of the Decisions dated 12 July 2007 and 28 April 2011). This strict way of conducting the proceedings is due to a change of R 30(3), as regards content, with respect to former R 27a(3) EPC 1973, which has been decided by the Administrative Council on December 7, 2006, as part of the amended implementing regulations to the EPC 2000. As can be seen from the travaux préparatoires of the Patent Law Committee, objections according to which the legal consequence of refusal was too strict or inappropriately tough, respectively, were countered by pointing out that complete sequence protocols filed in due time were indispensable for an appropriate European search report to be available in due time and that a request for further proceedings could be filed in case the time limit was missed (cf. CA/PL PV 30 Nr. 88-93 und CA/PL PV 31, Nr. 21-23).

[6] In the present case, on November 3, 2010, the RS requested the applicant to remedy deficiencies pursuant to R 30(3) by means of form 1128 […].

[7] This communication pointing out deficiencies (Mängelbescheid) did not criticize the first deficiency mentioned above (see point [4]) consisting in the use of feature keys for the numeric identifier <221> that were not foreseen [in WIPO-standard ST.25]. Moreover, the communication lacked precision because the deficiency (lacking numeric identifiers for artificial sequences) did not concern all the sequences but only sequences n° 9 to 11. Moreover, some indications were incorrect. The statement that in case of an artificial sequence the numeric identifier <221> was mandatory is wrong (see WIPO standard ST.25, point 30). Also, the designation “source” for the data element having numeric identifier <221> is incorrect (according to WIPO standard ST.25, Annex 1, the correct designation for <221> is “name/key”). Furthermore, the statement that the diskette that had been filed did not contain a sequence protocol is incomprehensible in view of the fact that both the sequence protocol and the rest of the application had been filed electronically.

[8] This notwithstanding the applicant has complied with the objections as far as they were comprehensible and correct. The amendments filed on November 11, 2010, did comply with the communication of the EPO insofar as the applicant had completed the data elements <223> for sequences n° 1 to 8 concerning artificial sequences and referred to the sequences n° 9 to 11, which it had originally referred to as artificial sequences in numeric identifier <213> by indicating plasmid designations.

[9] In a telephone interview, which apparently took place on January 21, 2011, i.e. more than two months after the filing of the corrected sequence protocol, the RS has again objected to deficiencies by informing the applicant that the sequence protocol did not give the description of the artificial sequences and that several feature keys used for numeric identifier <221> could not be acknowledged […].

[9.1] The first objection is not readily comprehensible because the corrected sequence protocol did not contain any more sequences referred to as artificial sequences in numeric identifier <213> without containing the then required data elements <220> and <223>. Perhaps the RS was of the opinion that the applicant had to continue to designate the sequences n° 9 to 11, which had been referred to as “artificial sequences” in numeric identifier <213> of the original sequence protocol, as such, i.e. that the applicant was not allowed to provide the relevant plasmid designations for sequences n° 9 to 11 in numeric identifier <213> and, thus, to avoid the indication of data elements that were actually required. If this is the background for the first objection raised in January 2011 – as it presumably is – the RS has gone beyond the objections raised at first.

[9.2] According to WIPO standard ST.25 (see points 25 and 30 as well as Annex 1, on <213>) [the applicant] shall provide either the scientific name of the organism or the indications “artificial sequence” or “unknown” in numeric identifier <213>. It is true that plasmids are not organisms in the narrow sense of the word, but they can of course have both a natural and an at least partially artificial origin. Moreover, there are many plasmid designations in molecular biology allowing the skilled person to unambiguously characterise [the plasmid] and which, therefore, comply with the purpose of the standard, i.e. to designate sequences as precisely as possible. In the framework of formal examination, to which the RS is in principle confined when examining sequence protocols, the indication of a plasmid designation in numeric identifier <213> cannot, as a rule, be objected to. The criticism that the sequence in a sequence protocol is in fact an artificial sequence, which has to be designated as such and which then has to be described using the numeric identifiers <220> and <223>, presupposes a technical examination of the facts for which the RS is not competent (see J 7/97 [8.1], which cites other decisions).

[9.3] The second objection raised during the telephone interview on January 21, 2011, concerned the deficiency of the sequence protocol which the RS had not mentioned in its communication pointing out deficiencies dated November 3, 2010, i.e. the use of several inappropriate feature keys in numeric identifier <221>. Insofar the RS has tried to introduce (“nachschieben”) by telephone an objection that had not been raised at first, concerning a deficiency that was there right from the beginning.

[10] In principle, the RS should take care that the invitation pursuant to R 30(3) addresses all objections, so that the applicant is prompted to quickly file a corrected sequence protocol that can be used for establishing the European search report. If in exceptional situations the situation is such that the sequence protocol filed in response to the invitation contains deficiencies that have not been objected to at first, the RS must not refuse the application without further ado, in application of R 30(3), second sentence and based on the original invitation, if the applicant has remedied the deficiencies that had been duly objected to, by filing a corrected sequence protocol, as he has done in the present case. Rather, the RS then has to send another written invitation to remedy the deficiencies.

Raising objections by telephone may be helpful in view of the relatively short time frame available for correcting the sequence protocol if the applicant then remedies the deficiencies objected to by telephone – on short notice. However, objections to deficiencies raised by telephone have no legal effect pursuant to R 30(3) because proceedings before the EPO are conducted in written form with the exception of cases where oral proceedings are foreseen (R 1 et seq.).

Therefore, in order to comply with the principle of the right to be heard (A 113(1)) it is necessary to send a second written communication pursuant to R 30(3) in such exceptional situations, and this communication has the legal consequence of triggering a fresh two-month time limit. However, the late furnishing fee only has to be paid once.

[11] In the present case the RS has committed a procedural violation by raising additional objections only orally, in the course of a telephone interview on January 21, 2011, which objections differed, as regards content, from the objections raised at first, which had been overcome by the applicant, without there being a second written communication. The original two-month period triggered by the communication pointing out deficiencies dated November 3, 2010, which had already expired at that time, could not have been relevant any more for remedying the deficiencies newly objected to by the RS.

[12] This notwithstanding, the applicant has tried again to remedy the objections by filing an amended sequence protocol. By filing an amended sequence protocol on January 26, 2011, the applicant took into account the new objection according to which several of the feature keys used for numeric identifier <221> could not be acknowledged. [The amended sequence protocol] only gave feature keys listed in Tables 5 and 6 of Annex 2 of the WIPO standard ST.25. It is true, however, that this amended sequence protocol also contained deficiencies because – apparently due to a software error – it contained a greater number of sequences than the original filing and because it did not contain the amendments concerning sequences n° 9 to 11 carried out on November 11, 2010.

[13] In this situation, the RS could not refuse the application without further ado by referring to its communication pointing out deficiencies dated November 3, 2010. The applicant had taken into account the then raised objections by the first correction dated November 11, 2010. Therefore, the original communication pointing out deficiencies could not have the legal consequences provided in R 30(3), second sentence, which means that the refusal of the application should not have been decided without a further communication pointing out deficiencies. Thus the impugned decision is based on a substantial procedural violation. Moreover, it is insufficiently reasoned because it does not deal at all with the attempts of the applicant to file a regular sequence protocol. This violation of R 111(2) constitutes a further substantial procedural violation.

[14] As a consequence of the procedural violations the impugned decision is to be set aside and the case is to be referred back to the first instance (A 111(1), second sentence, second alternative; Article 11 RPBA) and the appeal fee is to be reimbursed pursuant to R 103(1)(a).

[15] For the further proceedings before the RS the amended sequence protocol filed on March 11, 2011, will be relevant. In this context the Board of appeal points out the following:

• The deficiency concerning the inappropriate feature key for numeric identifier <221> appears to have been remedied.
• The fact that the DNA sequences n° 9 to 11 in numeric identifier <213> have not been designated as “artificial sequences” but have been defined in more detail by indicating plasmid designations is not to be objected to within the framework of the formal examination to be carried out by the RS […]
• In case of a subsequently filed sequence protocol, information concerning numeric identifiers <140> and <141> is mandatory. In contrast to the first amended sequence protocol filed on November 11, 2010, the sequence protocol filed on March 11, 2011, does not contain this information any more. This minor deficiency should be corrected by the EPO of its own motion (see also the Notice from the EPO dated 28 April 2011, point II.5, in the context of proceedings where the EPO acts as an international authority under the PCT).
• The applicant has not yet made the statement that the amended sequence protocol does not comprise any subject-matter extending beyond the application as originally filed (see Article 2(2) of the Decisions dated 12 July 2007 and 28 April 2011) for the sequence protocol filed on March 11, 2011.
• The applicant has already paid the fee for furnishing the sequence protocol belatedly.

Should you wish to download the whole decision (in German), just click here.

The decision having been anonymized (do not ask me why), I cannot give you a link to the file wrapper.